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USGS2024

Physics to fish—Understanding the factors that create and sustain native fish habitat in the San Francisco Estuary

Executive Summary The Bureau of Reclamation (Reclamation) operates the Central Valley Project (CVP), one of the nation’s largest water projects. Reclamation has an ongoing need to improve the scientific basis for adaptive management of the CVP and, by extension, joint operations with California’s State Water Project. The U.S. Geological Survey (USGS) works cooperatively with the Bureau of Reclamation to provide scientific support for the management of Reclamation’s CVP project. Major habitat restoration efforts and a new water-diversion point are planned to benefit delta smelt ( Hypomesus transpacificus ) and other species of concern while ensuring the reliability of water supply. In addition, various flow actions and management activities have been identified as possible methods to increase populations of delta smelt and salmonid ( Oncorhynchus spp.) runs of concern. The overarching goal of this cooperative project was to provide Reclamation with the scientific information needed to evaluate the efficacy of ongoing and future adaptive management actions and to improve the scientific basis for more flexible CVP operations that would achieve water-supply reliability and fish protection. The research and monitoring described in this report comprises the period 2015–19 and focuses on management issues related to native fish species of concern, especially delta smelt. Conserving the delta smelt population while providing a reliable water supply is a primary management and policy issue in California. Our approach for this cooperative project is based on the “physics to fish” concept, the idea that high-quality habitat is generated and sustained by the interaction between physical processes and the landscape. These interactions create a template for chemical and biological processes that can change across a variety of spatial and temporal scales. Following this concept, this project (hereafter referred to as “the physics to fish project”) included monitoring and studies of water flows, sediments, water quality, and invertebrate and fish dynamics across a range of spatial and temporal scales and in regions relevant to resource managers tasked with managing water supplies and ecosystem health in the San Francisco Estuary. The intent of this approach was to document the habitat conditions, important processes, and interactions among them that create high-quality habitat for native fishes so that the likely effects of future management actions (for example, habitat restoration) can be objectively assessed at the local (site-specific), regional (within subregions of the estuary), and landscape (across the entire estuary and beyond) scales. Hydrodynamically, the upper estuary (landward of Carquinez Strait) is characterized by a fixed volume of tidally exchanged water (for example, tidal prism) that interacts with the existing channel network and bathymetry to create regions with differing hydrodynamics. Our results indicate that careful study of construction or reoperation of existing infrastructure to perform management actions can help (1) improve the accuracy of hydrodynamic models; (2) further understanding of ecological effects; and (3) enhance abilities to predict ecological outcomes. At the local scale, we developed a new concept called the Lagrangian to Eulerian (LE) ratio that can be used as a tool for understanding the importance of various hydrodynamic processes in specific channels or channel networks and for forecasting transport dynamics. Channels with LE ratios<1 in a channel network or in a dead-end slough are hydrodynamically able to develop an exchange zone between two parcels of water that may have different chemical and physical properties. In a dead-end channel, there is a landward region with long residence time (no-exchange zone) and a seaward region with short residence time (high-exchange zone) that are well mixed with seaward waters. At the transition (exchange zone) between the high and no-exchange regions, a gradient will form in water-quality constituents that differ in concentration between the landward and seaward waters. Turbidity affects fish habitat and has declined through time in the San Francisco Estuary. Average turbidity across the Sacramento–San Joaquin Delta (hereafter referred to as “the Delta”) is dependent on annual hydrology. In dry years, the region around Cache Slough (known regionally as the “Cache Slough Complex”) in the northern Delta is generally more turbid than Suisun Bay and the lower Sacramento River. When the Yolo By-Pass (known regionally as “Yolo Bypass”), a large flood bypass that runs parallel to the Sacramento River in the northern Delta, is not flooding and river flows are lower, sediment is usually transported into the Cache Slough Complex because flood tides dominate ebb tides, resulting in transport of suspended sediment from seaward areas of the upper estuary into the Cache Slough Complex. These hydrodynamic conditions also favor the formation of turbidity maximums (TMs) in the Cache Slough Complex. The TMs are areas of higher suspended-sediment concentration, providing higher-turbidity habitat favored by some fishes, including delta smelt, and they can also concentrate other constituents, including phytoplankton and organic carbon that can be important in food webs. Pelagic primary production by phytoplankton is the basis for Delta food webs supporting pelagic fishes such as delta smelt; however, phytoplankton abundance in the Delta has declined during recent decades. We examined how nutrients, hydrodynamics, and other factors affect phytoplankton blooms. Based on our results, we developed three new concepts of phytoplankton bloom formation in the Delta, each associated with a distinct set of hydrologic conditions. First, productivity cascades highlighted how local processes can contribute to phytoplankton blooms observed at the regional scale. Second, we observed phytoplankton blooms in the upper San Francisco Estuary that were associated with transport out of Yolo By-Pass (transport blooms). Third, we also documented a series of phytoplankton blooms that were in the confluence area at the landward edge of Suisun Bay. The conditions leading to creation of confluence phytoplankton blooms are not yet understood, but the confluence region connects the Cache Slough Complex with Suisun Marsh. Therefore, blooms in this area have the potential to spread to large areas of the Delta. At the landscape scale, the distribution of the invasive clams ( Potamocorbula amurensis and Corbicula fluminea , hereafter referred to as “ Corbicula ”) is driven by salinity. At smaller spatial scales, the distribution of either species is sensitive to multiple factors affecting survival and reproduction, complicating efforts to predict distribution and abundance without considering local-scale conditions across the area of interest. In the Cache Slough Complex, the area landward of the exchange zone in regions with LE ratio<1 were characterized by low abundances of Corbicula probably because recruits from seaward areas are not transported past the exchange zone and because there are no landward tributaries with adult Corbicula to provide an upstream source of recruits. Corbicula biomass was highest near or downstream from the exchange zone consistent with Corbicula grazing on phytoplankton produced in the exchange zone or transported from the no-exchange zone. The severity of Corbicula grazing could be reduced by manipulating the hydrodynamic characteristics of waterways; however, the beneficial and harmful effects on the organisms meant to benefit from increased phytoplankton production, including zooplankton and fish species of concern, should be thoroughly examined before manipulating hydrodynamic characteristics. The distribution of fishes at the landscape scale is generally driven by the position of the salinity field in the estuary. The physics to fish project compared distributions of fishes at Ryer Island, a tidal wetland in Suisun Bay and a region of variable salinity, with fish distributions at the Cache Slough Complex, a freshwater region. At Ryer Island, there was an absence of freshwater invasive species and an abundance of native species, such as Sacramento splittail ( Pogonichthys macrolepidotus ), tule perch ( Hysterocarpus traskii ), and Sacramento pikeminnow ( Ptychocheilus grandis ). The native species were almost exclusively captured in wetland and nearshore shallow-water habitat regardless of water-quality conditions. In the Cache Slough Complex, our regional scale objective was to elucidate how hydrodynamic-physical habitat interactions drive fish-community structure. Our studies showed that dendritic channel systems were better able to support native species, while intertidal habitats supported those species best able to exploit the transient character of the habitat. Habitats upstream from the exchange zone were especially important in supporting high numbers of native fishes relative to within or downstream from the exchange zone. Many of the native species were associated with tidal marsh in the no-exchange zone. More pelagic-oriented, mobile species, such as Striped Bass ( Morone saxatilis ), threadfin shad ( Dorosoma petenense ), and Sacramento pikeminnow, were more affected by water-quality conditions, such as turbidity. The physics to fish concept developed in this project provides a framework for designing individual projects and for considering the cumulative effects of multiple projects in a region, using the LE ratio as a guiding metric. The physics to fish concept may also provide a suitable framework for coordinating management actions. Tidal wetlands can function in several ways in the hydrodynamic framework. Relatively small tidal wetlands with short channel networks and with LE ratios>1 are not able to maintain a landward no-exchange zone or an exchange zone. This likely means that any contributions to pelagic food webs would be limited to resources derived from wetland vegetation, which can include dissolved and particulate organic matter (detritus) and populations of consumers that can increase in abundance based on those resources. The fate of the contributed production from these channels depends on the characteristics of the receiving waters seaward of the tidal wetland. If these channels join a large system such as Suisun Bay, then any contribution is likely to be rapidly dispersed in the larger volume; however, the channel junction might provide a focal point for consumers, such as fishes, to congregate and feed on material leaving the wetland on ebb tides before it is dispersed in the larger volume. Fishes might also access these resources by entering the wetland. The physics to fish project has established a foundation and several new concepts for understanding how habitat restoration can benefit native fish populations at the local and regional levels. Many of the ideas regarding habitat restoration and channel modifications outlined in this report could help guide management actions that could improve conditions for native fishes at little or no water cost beyond water already dedicated to other management actions. A complete list of products originating from this work is provided in appendix 1.

California↗

USGS1961

Graphic and algebraic solutions of the discordant lead-uranium age problem

Uranium-bearing minerals that give lead-uranium and lead—lead ages that are essentially in agreement, i.e. concordant, generally are considered to have had a relatively simple geologic history and to have been unaltered since their deposition. The concordant ages obtained on such materials are, therefore, assumed to approach closely the actual age of the minerals. Many uranium-bearing samples, particularly uranium ores, give the following discordant age sequences; Pb 206 U 238 < Pb 207 U 235 ⪡ Pb 207 Pb 206 "> Pb 206 U 238 <Pb 207 U 235 ⪡Pb 207 Pb 206 or, less frequently, Pb 207 Pb 206 ⪡ Pb 207 U 235 < Pb 206 U 238 "> Pb 207 Pb 206 ⪡Pb 207 U 235 <Pb 206 U 238 . These discordant age sequences have been attributed most often to uncertainties in the common lead correction, selective loss of radio-active daughter products, loss or gain of lead or uranium, or contamination by an older generation of radiogenic lead. The evaluation of discordant lead isotope age data may be separated into two operations. The first operation, with which this paper is concerned, is mechanical in nature and involves the calculation of the different possible concordant ages corresponding to the various processes assumed to have produced the discordant ages. The second operation is more difficult to define and requires, in part, some personal judgement. It includes a synthesis of the possible concordant age solutions with other independent geologic and isotopic evidence. The concordant age ultimately chosen as most acceptable should be consistent not only with the known events in the geologic history of the area, the age relations of the enclosing rocks, and the mineralogic and paragenetic evidence, but also with other independent age measurements and the isotopic data obtained on the lead in related or associated non-radioactive minerals. The calculation of the possible concordant ages from discordant age data has been greatly simplified by Wetherill's graphical method of plotting the mole ratios of radiogenic Pb 206 U 238 "> Pb 206 U 238 ( N 206 N 238 "> N 206 N 238 ) vs. radiogenic Pb 207 U 235 "> Pb 207 U 235 ( N 207 N 235 "> N 207 N 235 ) after correcting for the contaminating common Pb 206 and Pb 207 . The linear relationships noted in this graphical procedure have been extended to plots of the mole ratios of total Pb 206 U 238 "> Pb 206 U 238 ( t N 206 N 238 "> t N 206 N 238 ) vs. total Pb 207 U 235 "> Pb 207 U 235 ( t N 207 N 235 "> t N 207 N 235 ). This modification permits the calculation of concordant ages for unaltered samples using only the Pb 207 Pb 206 "> Pb 207 Pb 206 ratio of the contaminating common lead. If isotopic data are available for two samples of the same age, x and y , from the same or related deposits or outcrops, graphs of the normalized difference ratios [ ( N 206 N 204 )x − ( N 206 N 204 )y ( N 238 N 204 )x −( N 238 N 204 )y ] vs. [ ( N 207 N 204 )x − ( N 207 N 204 )y ( N 235 N 204 )x −( N 235 N 204 )y ] "> [(N 206 N 204 )x − (N 206 N 204 )y(N 238 N 204 )x −(N 238 N 204 )y] vs. [(N 207 N 204 )x − (N 207 N 204 )y(N 235 N 204 )x −(N 235 N 204 )y] can give concordant ages corrected for unknown amounts of a common lead with an unknown Pb 207 / Pb 206 ratio. (If thorium is absent the difference ratios may be normalized with the more abundant index isotope, Pb 208 .) Similar plots of tho normalized, difference ratios for three genetically related samples ( x − y ) and( x − z ), will give concordant ages corrected, in addition, for either one unknown period of past alteration or initial contamination by an older generation of radiogenic lead of unknown Pb 207 /Pb 206 ratio. Practical numerical solutions for many of tho concordant age calculations are not currently available. However, the algebraic equivalents of these new graphical methods give equations which may be programmed for computing machines. For geologically probable parameters the equations of higher order have two positive real roots that rapidly converge on the exact concordant ages corrected for original radiogenic lead and for loss or gain of lead or uranium. Modifications of these general age equations expanded only to the second degree have been derived for use with desk calculators. These graphical and algebraic methods clearly suggest both the type and minimum number of samples necessary for adequate mathematical analysis of discordant lead isotope age data. This mathematical treatment also makes it clear that discordant lead isotope data alone cannot provide the basis for the choice of one of the possible concordant age solutions. The new equations, in particular, provide an incentive to improve our physical constants, analytical techniques and sampling methods in order that we may derive all of the useful geologic information that is available in a comprehensive lead isotope age study.

Geochimica et Cosmochimica Acta↗

USGS2011

Range-wide assessment of livestock grazing across the sagebrush biome

Domestic livestock grazing occurs in virtually all sagebrush habitats and is a prominent disturbance factor. By affecting habitat condition and trend, grazing influences the resources required by, and thus, the distribution and abundance of sagebrush-obligate wildlife species (for example, sage-grouse Centrocercus spp.). Yet, the risks that livestock grazing may pose to these species and their habitats are not always clear. Although livestock grazing intensity and associated habitat condition may be known in many places at the local level, we have not yet been able to answer questions about use, condition, and trend at the landscape scale or at the range-wide scale for wildlife species. A great deal of information about grazing use, management regimes, and ecological condition exists at the local level (for individual livestock management units) under the oversight of organizations such as the Bureau of Land Management (BLM). However, the extent, quality, and types of existing data are unknown, which hinders the compilation, mapping, or analysis of these data. Once compiled, these data may be helpful for drawing conclusions about rangeland status, and we may be able to identify relationships between those data and wildlife habitat at the landscape scale. The overall objective of our study was to perform a range-wide assessment of livestock grazing effects (and the relevant supporting data) in sagebrush ecosystems managed by the BLM. Our assessments and analyses focused primarily on local-level management and data collected at the scale of BLM grazing allotments (that is, individual livestock management units). Specific objectives included the following: 1. Identify and refine existing range-wide datasets to be used for analyses of livestock grazing effects on sagebrush ecosystems. 2. Assess the extent, quality, and types of livestock grazing-related natural resource data collected by BLM range-wide (i.e., across allotments, districts and regions). 3. Compile and synthesize recommendations from federal and university rangeland science experts about how BLM might prioritize collection of different types of livestock grazing-related natural resource data. 4. Investigate whether range-wide datasets (Objective 1) could be used in conjunction with remotely sensed imagery to identify across broad scales (a) allotments potentially not meeting BLM Land Health Standards (LHS) and (b) allotments in which unmet standards might be attributable to livestock grazing. Objective 1: We identified four datasets that potentially could be used for analyses of livestock grazing effects on sagebrush ecosystems. First, we obtained the most current spatial data (typically up to 2007, 2008, or 2009) for all BLM allotments and compiled data into a coarse, topologically enforced dataset that delineated grazing allotment boundaries. Second, we obtained LHS evaluation data (as of 2007) for all allotments across all districts and regions; these data included date of most recent evaluation, BLM determinations of whether region-specific standards were met, and whether BLM deemed livestock to have contributed to any unmet standards. Third, we examined grazing records of three types: Actual Use (permittee-reported), Billed Use (BLM-reported), and Permitted Use (legally authorized). Finally, we explored the possibility of using existing Natural Resources Conservation Service (NRCS) Ecological Site Description (ESD) data to make up-to-date estimates of production and forage availability on BLM allotments. Objective 2: We investigated the availability of BLM livestock grazing-related monitoring data and the status of LHS across 310 randomly selected allotments in 13 BLM field offices. We found that, relative to other data types, the most commonly available monitoring data were Actual Use numbers (permittee-reported livestock numbers and season-of-use), followed by Photo Point, forage Utilization, and finally, Vegetation Trend measurement data. Data availability and frequency of data collection varied across allotments and field offices. Analysis of the BLM's LHS data indicated 67 percent of allotments analyzed were meeting standards. For those not meeting standards, livestock were considered the causal factor in 45 percent of cases (about 15 percent of all allotments). Objective 3: We sought input from 42 university and federal rangeland science experts about how best to prioritize rangeland monitoring activities associated with ascertaining livestock impacts on vegetation resources. When we presented a hypothetical scenario to these scientists and asked them to prioritize monitoring activities, the most common response was to measure ground and vegetation cover, a variable that in many cases (10 of 13 field offices sampled) BLM had already identified as a monitoring priority. Experts identified several other traditional (for example, photo points) and emerging approaches (for example, high-resolution aerial photography) to monitoring. Objective 4: We used spatial allotment data (described in Objective 1) and remotely sensed vegetation data (sagebrush cover, herbaceous vegetation cover, litter and bare soil) to assess differences in allotment LHS status ("Not met" vs. "Met"; if "Not met" - livestock-caused vs. not). We then developed logistic regression models, using vegetation variables to predict LHS status of BLM allotments in sagebrush steppe habitats in Wyoming and portions of Montana and Colorado. In general, we found that more consistent data collection at the local level might improve suitability of data for broad-scale analyses of livestock impacts. As is, data collection methodologies varied across field offices and States, and we did not find any local-level monitoring data (Actual Use, Utilization, Vegetation Trend) that had been collected consistently enough over time or space for range-wide analyses. Moreover, continued and improved emphasis on monitoring also may aid local management decisions, particularly with respect to effects of livestock grazing. Rangeland science experts identified ground cover as a high monitoring priority for assessing range condition and emphasized the importance of tracking livestock numbers and grazing dates. Ultimately, the most effective monitoring program may entail both increased data collection effort and the integration of alternative monitoring approaches (for example, remote sensing or monitoring teams). In the course of our study, we identified three additional datasets that could potentially be used for range-wide analyses: spatial allotment boundary data for all BLM allotments range-wide, LHS evaluations of BLM allotments, and livestock use data (livestock numbers and grazing dates). It may be possible to use these spatial datasets to help prioritize monitoring activities over the extensive land areas managed by BLM. We present an example of how we used spatial allotment boundary data and LHS data to test whether remotely sensed vegetation characteristics could be used to predict which allotments met or did not meet LHS. This approach may be further improved by the results of current efforts by BLM to test whether more intensive (higher resolution) LHS assessments more accurately describe land health status. Standardized data collection in more ecologically meaningful land units may improve our ability to use local-level data for broad-scale analyses.

Open-File Report↗

USGS2016

Users and uses of Landsat 8 satellite imagery—2014 survey results

Executive Summary In 2013, Landsat 8 began adding high quality, global, moderate-resolution imagery to the more than 40-year archive of Landsat imagery. To assess the potential effects of the availability of Landsat 8 imagery on users and their work, the U.S. Geological Survey (USGS) Land Remote Sensing Program (LRS) initiated a survey of Landsat users. The objectives of the survey were to 1. Characterize various Landsat user groups, such as United States (U.S.) and international users and Landsat 8 and non-Landsat 8 users; 2. Identify any differences among user groups in uses and preferences; 3. Measure the importance of and satisfaction with Landsat 8 attributes; 4. Assess the importance to users of the frequency of usable imagery; and 5. Determine any challenges in using Landsat 8. The online survey was sent to 51,617 Landsat users registered with USGS in May 2014. Almost 13,000 people responded to the survey for a response rate of 25 percent (n = 12,966). Current Landsat users (users who had used Landsat in their work in the year prior to the survey) composed 89 percent of the sample (n = 11,549) and past Landsat users composed 11 percent (n = 1,417). The results reported here apply to current Landsat users registered with the USGS Earth Resources Observation and Science (EROS) Center. Users from 161 countries responded to the survey. Of those, 19 percent were citizens or permanent residents of the United States and 81 percent resided in other countries. More than 70 percent of current users had used Landsat 8 in the year prior to the survey. The majority of Landsat 8 users (65 percent) were established users who used Landsat imagery regularly both before and after Landsat 8 imagery became available. The average current Landsat user was male, 36 years old, and highly educated, with 9 years of experience using satellite imagery or geographic information system (GIS) software. Landsat 8 users had, on average, two more years of experience than non-Landsat 8 users. Users were employed predominantly by academic institutions (65 percent), followed by private businesses (13 percent), Federal governments (10 percent), State and local governments (6 percent), and nonprofit organizations (6 percent). Of the Landsat imagery obtained in the past year by current users, on average 31 percent came from a Landsat 8 sensor. An equivalent amount came from the Landsat 7 ETM+ sensor (33 percent); slightly less came from Landsats 4 and 5 TM sensors (27 percent). Much less came from Landsats 1 through 5 MSS sensors (5 percent). Overall, more than a third of users’ work used Landsat imagery (38 percent). Of this work, on average, 37 percent of the work was operational. Landsat 8 users considered a greater proportion of their work operational than non-Landsat 8 users (39 percent compared with 29 percent). Environmental sciences and management were the most commonly selected primary applications (selected by 42 percent of users). Land use/land cover (23 percent) was the second most commonly selected primary application, followed by education (12 percent), agriculture (9 percent), and planning and development (6 percent). Landsat 8 users were asked to rank the importance of certain attributes in determining whether to use Landsat 8 imagery in their work. The archive was ranked most important, followed by cost, spatial resolution, extent of coverage, data quality, and frequency of revisit. Users were asked how satisfied they were with these same attributes as they currently apply to Landsat 8 imagery. On average, users were most satisfied with lack of cost, extent of coverage, data quality, and the archive, but they were satisfied with all attributes. Users were asked how often they needed Landsat imagery to meet various requirements for their primary application. The survey question specifically asked how often users needed usable imagery, which differs from how often they would like the Landsat satellites to acquire an image. Users were asked to identify their needed frequency of usable imagery for the following levels: 1. Threshold level—the minimum frequency of usable imagery needed to be of any value to their primary application. 2. Breakthrough level—the frequency of usable imagery that would result in a significant improvement for their primary application of the imagery. 3. Target level—the frequency of usable imagery that would only provide a limited additional increase in the expected performance for their primary application. To meet the threshold level, three-quarters of users needed usable imagery every 17 days or less frequently. At the breakthrough level, two-thirds of users (64 percent) needed a usable image every 5–16 days. The current constellation of two satellites (Landsat 7 and 8) is capable of meeting the threshold and breakthrough needs of most users at least some of the time, but a single satellite would be highly unlikely to do so. Two-fifths of users (40 percent) felt that usable imagery provided every 4 days or more frequently would meet their target level which the current Landsat constellation cannot provide. Landsat 8 users were significantly more likely than non-Landsat 8 users to need usable imagery more frequently to meet their target levels. Additionally, U.S. Landsat 8 users were significantly more likely than other Landsat users to need usable imagery more frequently in order meet both their breakthrough and target levels. To explore the effect of the availability of Landsat 8 imagery on Landsat imagery use in general, established users (those who had consistently used Landsat imagery both before and after Landsat 8 imagery became available) using Landsat 8 imagery were asked about changes in the amount of Landsat imagery they used. The majority of established users using Landsat 8 imagery (60 percent) reported an average increase of 51 percent in the number of scenes obtained after Landsat 8 imagery became available. Landsat 8 users were asked if they had encountered challenges in using Landsat 8 whereas non-Landsat 8 users were asked if such challenges had played a role in why they were not using Landsat 8 imagery. Although many users did not encounter challenges when using or trying to use Landsat 8 data, slightly less than 30 percent did encounter issues with processing the data to a usable point. The most common issue reported was not being able to create or have access to a surface reflectance corrected product. Other challenges were related to the file sizes of images being too large to download, store, or analyze. There were no statistically significant differences between Landsat 8 and non-Landsat 8 users in terms of challenges encountered when using or trying to use the imagery, which indicates that users were not unduly discouraged by the challenges they may have encountered. When asked about potential consequences of not using Landsat 8, more than half of the non-Landsat 8 users did not report detrimental effects on their work from not using the imagery. Of those who did report detrimental effects, decreased quality of work, decreased scope of work, and increased time spent on work were the most common.

Open-File Report↗

USGS2012

Evaluating prediction uncertainty of areas contributing recharge to well fields of multiple water suppliers in the Hunt-Annaquatucket-Pettaquamscutt River Basins, Rhode Island

Three river basins in central Rhode Island-the Hunt River, the Annaquatucket River, and the Pettaquamscutt River-contain 15 production wells clustered in 4 pumping centers from which drinking water is withdrawn. These high-capacity production wells, operated by three water suppliers, are screened in coarse-grained deposits of glacial origin. The risk of contaminating water withdrawn by these well centers may be reduced if the areas contributing recharge to the well centers are delineated and these areas protected from land uses that may affect the water quality. The U.S. Geological Survey, in cooperation with the Rhode Island Department of Health, began an investigation in 2009 to improve the understanding of groundwater flow and delineate areas contributing recharge to the well centers as part of an effort to protect the source of water to these well centers. A groundwater-flow model was calibrated by inverse modeling using nonlinear regression to obtain the optimal set of parameter values, which provide a single, best representation of the area contributing recharge to a well center. Summary statistics from the calibrated model were used to evaluate the uncertainty associated with the predicted areas contributing recharge to the well centers. This uncertainty analysis was done so that the contributing areas to the well centers would not be underestimated, thereby leaving the well centers inadequately protected. The analysis led to contributing areas expressed as a probability distribution (probabilistic contributing areas) that differ from a single or deterministic contributing area. Groundwater flow was simulated in the surficial deposits and the underlying bedrock in the 47-square-mile study area. Observations (165 groundwater levels and 7 base flows) provided sufficient information to estimate parameters representing recharge and horizontal hydraulic conductivity of the glacial deposits and hydraulic conductance of streambeds. The calibrated value for recharge to valley-fill deposits was 27.3 inches per year (in/yr) and to upland till deposits was 18.7 in/yr. Calibrated values for horizontal hydraulic conductivity of the valley-fill deposits ranged from 20 to 480 feet per day (ft/d) and of the upland till deposits was 16.2 ft/d. Calibrated values of streambed hydraulic conductance ranged from 10,000 to 52,000 feet squared per day. Values of recharge and horizontal hydraulic conductivity of the valley-fill deposits were the most precisely estimated, whereas the horizontal hydraulic conductivity of till deposits was the least precisely estimated. Simulated areas contributing recharge to the well centers on the basis of the calibrated model ranged from 0.19 to 1.12 square miles (mi 2 ) and covered a total area of 2.79 mi 2 for average well center withdrawal rates during 2004-08 (235 to 1,858 gallons per minute (gal/min)). Simulated areas contributing recharge for the maximum well center pumping capacities (800 to 8,500 gal/min) ranged from 0.37 to 3.53 mi2 and covered a total area of 7.99 mi2 in the modeled area. Simulated areas contributing recharge extend upgradient of the well centers to upland till and to groundwater divides. Some areas contributing recharge include small, isolated areas remote from the well centers. Relatively short groundwater traveltimes from recharging locations to discharging wells indicated the wells are vulnerable to contamination from land-surface activities: median traveltimes ranged from 2.9 to 5.0 years for the well centers, and 78 to 93 percent of the traveltimes were 10 years or less for the well centers. Land cover in the areas contributing recharge includes a substantial amount of urban land use for the two well centers in the Hunt River Basin, agriculture and sand and gravel mining uses for the well center in the Annaquatucket River Basin, and, for the well center in the Pettaquamscutt River Basin, land use is primarily undeveloped. Model-prediction uncertainty was evaluated using a Monte Carlo analysis. The parameter variance-covariance matrix from nonlinear regression was used to create parameter sets that reflect the uncertainty of the parameter estimates and the correlation among parameters. The remaining parameters representing the glacial deposits (vertical anisotropy of valley-fill deposits and of till deposits, maximum groundwater evapotranspiration, and hydraulic conductance for headdependent cells representing a groundwater divide) that could not be estimated with nonlinear regression were incorporated into the variance-covariance matrix using prior information on parameters. Thus the uncertainty analysis was an outcome of calibrating the parameters to available observations and to information that the modeler provided. A water budget and model-fit statistical criteria were used to assess parameter sets so that prediction uncertainty was not overestimated. Because of the effects of parameter uncertainty, the size of the probabilistic contributing areas for each well center for both average and maximum pumping rates was larger than the size of the deterministic contributing areas for the well center. Thus, some areas not in the deterministic contributing area may actually be in the contributing area, including additional areas of urban and agricultural land use. Generally, areas closest to the well centers with short groundwater traveltimes are associated with higher probabilities, whereas areas distant from the well centers with long groundwater traveltimes are associated with lower probabilities. The deterministic contributing areas generally corresponded to areas associated with high probabilities (greater than 50 percent). Areas associated with low probabilities extended long distances along groundwater divides in the uplands remote from the well centers.

Rhode Island↗

USGS1983

Ground water in the southeastern Uinta Basin, Utah and Colorado

The potential for developing oil-shale resources in the southeastern Uinta Basin of Utah and Colorado has created the need for information on the quantity and quality of water available in the area. This report describes the availability and chemical quality of ground water, which might provide a source or supplement of water supply for an oil-shale industry. Ground water in the southeastern Uinta Basin occurs in three major aquifers. Alluvial aquifers of small areal extent are present in valley-fill deposits of six major drainages. Consolidated-rock aquifers include the bird's-nest aquifer in the Parachute Creek Member of the Green River Formation, which is limited to the central part of the study area; and the Douglas Creek aquifer, which includes parts of the Douglas Creek Member of the Green River Formation and parts of the intertonguing Renegade Tongue of the Wasatch Formation; this aquifer underlies most of the study area. The alluvial aquifers are recharged by infiltration of streamflow and leakage from consolidated-rock aquifers. Recharge is estimated to average about 32,000 acre-feet per year. Discharge from alluvial aquifers, primarily by evapotranspiration, also averages about 32,000 acre-feet per year. The estimated volume of recoverable water in storage in alluvial aquifers is about 200,000 acre-feet. Maximum yields to individual wells are less than 1,000 gallons per minute. Recharge to the bird's-nest aquifer, primarily from stream infiltration and downward leakage from the overlying Uinta Formation, is estimated to average 670 acre-feet per year. Discharge from the bird's-nest aquifer, which is primarily by seepage to Bitter Creek and the White River, is estimated to be 670 acre-feet per year. The estimated volume of recoverable water in storage in the bird's-nest aquifer is 1.9 million acre-feet. Maximum yields to individual wells in some areas may be as much as 5,000 gallons per minute. A digital-computer model of the flow system was used to evaluate the effects of oil-shale development on the bird's-nest aquifer at the Federal lease tracts Ua and Ub. Results of model simulations indicate that during construction of a vertical access shaft, a pumping rate of about 900 gallons per minute would be required to dewater the aquifer. The model also indicates that the construction of a proposed reservoir on the White River may raise water levels in the bird's-nest aquifer near the reservoir site by as much as 45 feet. The flow model was used to evaluate the potential ground-water supply available for oil-shale development in the vicinity of the Federal lease tracts Ua and Ub. The results of the simulation indicate that the bird's-nest aquifer could supply about 10,000 acre-feet of water per year at that site, for a period of 20 years. Drawdown after 20 years of pumping would exceed 250 feet near the simulated well field. Based on the results of the model simulation, it is estimated that the aquifer could simultaneously supply another 10,000 acre-feet of water per year in the northern part of the study area, but some interference between well fields could be expected. The Douglas Creek aquifer is recharged by precipitation and stream infiltration at an average rate of about 20,000 acre-feet per year. Discharge is estimated to be about the same and is primarily through springs and diffuse seepage. The estimated volume of recoverable water in storage is 16 million acre-feet. Maximum yields to individual wells are estimated to be less than 500 gallons per minute. A model of the flow system in the Douglas Creek aquifer indicates that the aquifer could supply about 700 acre-feet of water per year for oil-shale development at Federal lease tracts Ua and Ub and at the TOSCO Corp. site. After 20 years of pumping, water levels in production wells would be near the base of the aquifer. Based on the results of the model simulation, it is estimated that the aquifer could supply another 700 acre-feet of water per year in the southern part of the modeled area, but some interference between wells could be expected. Chemical quality of the ground water in the southeastern Uinta Basin varies considerably. Water from alluvial wells ranges from about 440 to 27,800 milligrams per liter of dissolved solids. Water from two consolidated- rock aquifers has dissolved-solids concentrations ranging from 870 to 5,810 milligrams per liter in the bird's-nest aquifer, and from 640 to 6,100 milligrams per liter in the Douglas Creek aquifer. Water from alluvial wells generally is a sodium sulfate type, whereas water in both the consolidated- rock aquifers generally changes from a sodium sulfate type to a sodium bicarbonate type. All ground water is very alkaline, and the alluvial aquifers contain very hard water. None of the water is suitable for public supply, but all the water could be used for industrial purposes such as washing and cooling. Changes in chemical composition of the ground water can be attributed to several physiochemical processes, including mineral precipitation and dissolution, oxidation and reduction, mixing, ion exchange, and evaporative concentration. Mass-transfer modeling of these processes shows how they can account for the variability in the ground-water quality. The mass-transfer model of the Bitter Creek alluvial aquifer shows that evaporative concentration, combined with precipitation of calcite, dolomite, gypsum, and release of carbon dioxide to the atmosphere results in the documented changes in pH and dissolved solids in the water. The water-quality changes in the consolidated-rock aquifers are a result of precipitation of calcium carbonate and perhaps dolomite (calcium magnesium carbonate) with the reduction of sulfate by organic carbon, as well as ion exchange of magnesium for sodium. These processes result in large values of pH and alkalinity in the water.

Colorado, Utah↗

USGS1987

Ground water in the southeastern Uinta Basin, Utah and Colorado

The potential for developing oil-shale resources in the southeastern Uinta Basin of Utah and Colorado has created the need for information on the quantity and quality of water available in the area. This report describes the availability and chemical quality of ground water, which might provide a source or supplement of water supply for an oil-shale industry. Ground water in the southeastern Uinta Basin occurs in three major aquifers. Alluvial aquifers of small areal extent are present i n val ley-f i 11 deposits of six major drainages. Consolidated-rock aquifers include the birds's-nest aquifer i n the Parachute Creek Member of the G reen River Formation, which is limited to the central part of the study area; and the Douglas Creek aquifer, which includes parts of the Douglas Creek Member of the Green River Formation and parts of the intertonguing Renegade Tongue of the Wasatch Formation; this aquifer underlies most of the study area. The alluvial aquifers are recharged by infiltration of streamflow and leakage from consolidated-rock aquifers. Recharge is estimated to average about 32,000 acre-feet per year. Discharge from alluvial aquifers, primarily by evapotranspiration, also averages about 32,000 acre-feet per year. The estimated volume of recoverable water in storage in alluvial aquifers is about 200,000 acre-feet. Maximum yields to individual wells are less than 1,000 gallons per minute. Recharge to the bird's-nest aquifer, primarily from stream infiltration and downward leakage from the overlying Uinta Formation, is estimated to average 670 acre-feet per year. Discharge from the bird's-nest aquifer, which is primarily by seepage to Bitter Creek and the White River, is estimated to be at 670 acre-feet per year. The estimated volume of recoverable water in storage in the bird's-nest aquifer is 1.9 million acre-feet. Maximum yields to individual wells in some areas may be as much as 5,000 gallons per minute. A digital-computer model of the flow system was used to evaluate the effects of oil-shale development on the bird's-nest aquifer at the Federal lease tracts Ua and Ub. Results of model simulations indicate that during construction of a vertical access shaft, a pumping rate of about 900 gallons per minute would be required to dewaterthe aquifer. The model also indicates that the construction of a proposed reservoir on the White River may raise water levels in the bird's-nest aquifer near the reservoir site by as much as 45 feet. The flow model was used to evaluate the potential ground-water supply available for oil-shale development in the vicinity of the Federal lease tracts Ua and Ub. The results of the simulation indicate that bird's-nest aquifer could supply about 10,000 acre-feet of water per year at that site, for a period of 20 years. Downdraw after 20 years of pumping would exceed 250 feet near the simulated well field. Based on the results of the model simulation, it is estimated that the aquifer could simultaneously supply another 10,000 acre-feet of water per year in the northern part of the study area, but some interference between well fields could be expected. The Douglas Creek aquifer is recharged by precipitation and stream infiltration at an average rate of about 20.000 acre-feet per year. Discharge is estimated to be about the same and is primarily through springs and diffuse seepage. The estimated volume of recoverable water in storage is 16 million acre-feet. Maximum yields to individual wells are estimated to be less than 500 gallons per minute. A model of the flow system in the Douglas Creek aquifer indicates that the aquifer could supply about 700 acre-feet of water per year for oil-shale development at Federal lease tracts Ua and Ub and at the TOSCO Corp. site. After 20 years of pumping, water levels in production wells would be near the base of the aquifer. Based on the results of the model simulation, it is estimated that the aquifer could supply another 700 acre-feet of water per year in the southern part of the modeled area, but some interference between wells could be expected. Chemical quality of the ground water in the southeastern Uinta Basin varies considerably. Water from alluvial wells ranges from about 440 to 27,800 milligrams per liter of dissolved solids. Water from two consolidated-rock aquifers has dissolved-solids concentrations ranging from 870 to 5,810 milligrams per liter in the bird's-nest aquifer, and from 640 to 6,100 milligrams per liter in the Douglas Creek aquifer. Water from alluvial wells generally is a sodium sulfate type, whereas water in both the consolidated-rock aquifers generally changes from a sodium sulfate type to a sodium bicarbonate type. All ground water is very alkaline, and the alluvial aquifers contain very hard water. None of the water is suitable for public supply, but all the water could be used for industrial purposes such as washing and cooling. Changes in chemical composition of the ground water can be attributed to several physiochemical processes, including mineral precipitation and dissolution, oxidation and reduction, mixing, ion exchange, and evaporative concentration. Mass-transfer modeling of these processes shows how they can account for the variability in the ground-water quality. The mass-transfer model of the Bitter Creek alluvial aquifer shows that evaporative concentration, combined with precipitation of calcite, dolomite, gypsum, and release of carbon dioxide to the atmosphere results in the documented changes in the pH and dissolved solids in the water. The water-quality changes in the consolidated-rock aquifers are a result of precipitation of calcium carbonate and perhaps dolomite (calcium magnesium carbonate) with the reduction of sulfate by organic carbon, as well as ion exchange of magnesium for sodium. These processes result in large values of pH and alkalinity in the water.

Colorado, Utah↗

USGS2012

USGS Environmental health science strategy: providing environmental health science for a changing world: Public review release

America has an abundance of natural resources. We have bountiful clean water, fertile soil, and unrivaled national parks, wildlife refuges, and public lands. These resources enrich our lives and preserve our health and wellbeing. These resources have been maintained because of our history of respect for their value and an enduring commitment to their vigilant protection. Awareness of the social, economic, and personal value of the health of our environment is increasing. The emergence of environmentally driven diseases caused by environmental exposure to contaminants and pathogens is a growing concern worldwide. New health threats and patterns of established threats are affected by both natural and anthropogenic changes to the environment. Human activities are key drivers of emerging (new and re-emerging) health threats. Societal demands for land and natural resources, a better quality of life, improved economic prosperity, and the environmental impacts associated with these demands will continue to increase. Natural earth processes, climate trends, and related climatic events will add to the environmental impact of human activities. These environmental drivers will influence exposure to disease agents, including viral, bacterial, prion, and fungal pathogens, parasites, natural earth materials, toxins and other biogenic compounds, and synthetic chemicals and substances. The U.S. Geological Survey (USGS) defines environmental health science broadly as the interdisciplinary study of relations among the quality of the physical environment, the health of the living environment, and human health. The interactions among these three spheres are driven by human activities, ecological processes, and natural earth processes; the interactions affect exposure to contaminants and pathogens and the severity of environmentally driven diseases in animals and people. This definition provides USGS with a framework for synthesizing natural science information from across the Bureau and providing it to environmental, natural resource, agricultural, and public-health managers. The USGS is a Federal science agency with a broad range of natural science expertise relevant to environmental health. USGS provides scientific information and tools as a scientific basis for management and policy decision making. USGS specializes in science at the environment-health interface, by characterizing the processes that affect the interaction among the physical environment, the living environment, and people, and the resulting factors that affect ecological and human exposure to disease agents. This report describes a 10-year strategy that encompasses the portfolio of USGS environmental health science. It summarizes national environmental health priorities that USGS is best suited to address, and will serve as a strategic framework for USGS environmental health science goals, actions, and outcomes for the next decade. Implementation of this strategy is intended to aid coordination of USGS environmental health activities and to provide a focal point for disseminating information to stakeholders. The "One Health" paradigm advocated by the World Health Organization (WHO, 2011), and the American Veterinary Medicine Association (AVMA, 2008), among others, is based on a general recognition that the health of humans, animals, and the environment are inextricably linked. Thus, successful efforts to protect that health will require increased interdisciplinary research and increased communication and collaboration among the broader scientific and health community. This strategy is built upon that paradigm. The vision, mission, and five cornerstone goals of the USGS Environmental Health Science Strategy were developed with significant input from a wide range of stakeholders. Vision - The USGS is a premier source of the environmental health science needed to safeguard the health of the environment, fish, wildlife, and people. Mission - The mission of USGS in environmental health science is to contribute scientific information to environmental, natural resource, agricultural, and public-health managers, who use that science to support sound decision making. USGS provides the science to: - Goal 1: Identify, prioritize, and detect contaminants and pathogens of emerging environmental concern. - Goal 2: Reduce the impact of contaminants on the environment, fish, wildlife, and people. - Goal 3: Reduce the impact of pathogens on the environment, fish, wildlife, and people. - Goal 4: Discover the complex interactions and combined effects of exposure to contaminants and pathogens. - Goal 5: Prepare for and respond to environmental impacts and related health threats of natural and anthropogenic disasters. Goals 1 through 4 are intended to provide science to address environmental health threats in a logical order, from informing prevention and preparedness, to supporting systematic management response to environmental health issues. Goal 4 addresses the interaction among contaminants and pathogens, an issue of emerging concern in environmental health science. Goal 5 acknowledges the fact that natural and anthropogenic disasters can cause immediate and prolonged adverse environmental health threats. This strategy proposes that USGS take the following strategic science actions to achieve each of the five goals of this strategy: Goal 1: Identify, prioritize, and detect contaminants and pathogens of emerging environmental concern. - Strategic Science Action 1. - Prioritize contaminants and pathogens of emerging concern to guide research, detection, and management activities. - Strategic Science Action 2. - Conduct surveillance and monitoring to provide early warning of emerging health threats. - Strategic Science Action 3. - Develop approaches and tools that identify vulnerable environmental settings, ecosystems, and species. Goal 2: Reduce the impact of contaminants on the environment, fish, wildlife, and people. - Strategic Science Action 1. - Systematically characterize the sources, occurrence, transport and fate of environmental contaminants to guide efforts to manage and mitigate contamination. - Strategic Science Action 2. - Evaluate the threats of contamination on the health of the environment, fish, wildlife, and people, and inform the associated management and protection efforts. - Strategic Science Action 3. - Characterize potential human exposure to support establishment of health-based standards or guidelines and contamination-reduction efforts. Goal 3: Reduce the impact of pathogens on the environment, fish, wildlife, and people. - Strategic Science Action 1. - Determine the biotic and abiotic factors that control the ecology of infectious diseases affecting natural populations of aquatic and terrestrial species and potential transmission to other animals and humans. - Strategic Science Action 2. - Establish how natural and anthropogenic environmental changes affect the distribution and severity of infectious diseases in natural populations of aquatic and terrestrial species and potential transmission to other animals and humans. - Strategic Science Action 3. - Develop surveillance systems to identify changing patterns of disease activity in priority geographic areas. Goal 4: Discover the complex interactions and combined effects of exposure to contaminants and pathogens. - Strategic Science Action 1. - Identify how exposure to one class of disease agents (contaminants or pathogens) can make an organism more susceptible to effects from exposure to the other class of disease agents. - Strategic Science Action 2. - Implement interdisciplinary studies that characterize the effects of combined exposure to pathogens and contaminants. Goal 5: Prepare for and respond to the environmental impacts and related health threats of natural and anthropogenic disasters. - Strategic Science Action 1. - Establish a formal interdisciplinary science capability to rapidly assess the environmental health risks associated with disasters. - Strategic Science Action 2. - Enhance methods to anticipate, prepare for, and identify environmental, ecological, and related health impacts of future disasters. This strategy is one of seven USGS science strategies developed concurrently: - Climate and Land Use Change - Core Science Systems - Ecosystems - Energy and Mineral Resources - Environmental Health - Natural Hazards - Water. This strategy describes how USGS will address the highest priority environmental health issues facing the Nation. The ultimate intended outcome of this science strategy is prevention and reduction of adverse impacts to the quality of the environment, the health of our living resources, and human health. Communication with, and receiving input from, partners and stakeholders regarding their science needs is essential for successful implementation of this strategy. It is incumbent on USGS to reach out to all stakeholders to ensure that USGS efforts are focused on the highest priority environmental health issues and that products are provided in the most timely and usable form to all those who can use them. USGS must reach out to the scientific community, internally and externally, to ensure that our efforts are integrated with and take full advantage of the activities of others.

Open-File Report↗

USGS1999

The ecological condition of estuaries in the Gulf of Mexico

The Gulf of Mexico is a vast natural resource encompassing the coastal areas of western Florida, Alabama, Mississippi, Louisiana, and Texas, as well as a portion of Mexico. Many estuaries flow into the Gulf of Mexico and serve as nursery grounds for fish, habitat for a wide variety of wildlife, shipping routes, and a source of recreation. Estuarine-dependent species constitute more than 95 percent of the commercial fishery harvests from the Gulf of Mexico, and many important recreational fishery species depend on estuaries during some part of their life cycle. Gulf estuaries are diverse and productive ecosystems that provide a variety of valuable resources, including fish and shellfish, recreation, transportation, and water supply. Assessing the overall condition of Gulf of Mexico estuaries required incorporating data from other federal, state, and local monitoring programs to augment the information on ecological indicators collected by the U.S. Environmental Protection Agency’s (USEPA) Environmental Monitoring and Assessment Program (EMAP). The resulting document would provide a synthesis of the available knowledge about the condition of Gulf of Mexico estuaries. This document is intended for use by scientists and other citizens concerned with the ecological condition of estuaries, as well as by managers and lawmakers interested in the sustained use of estuaries for commercial and recreational purposes. It also addresses public concerns about the aesthetic quality of coastal areas vital to tourism and recreation. By producing this report on the ecological condition of estuaries in the Gulf of Mexico, we have taken one step in assessing the health of this environmental resource. We have produced an environmental “report card” to be used as a guide in the evaluation of management decisions and research directions. This report is organized in three parts: (1) an introduction that gives background information on the Gulf of Mexico, estuarine ecology, and the factors that impact estuaries in the gulf, (2) the main section on priority ecological indicators used to measure the condition of estuaries in the gulf and (3) an ecological report card that summarizes the data on ecological indicators and provides a rating of the condition of estuaries in each gulf state and for gulf estuaries overall. Many of the ratings were based on the percent area of estuaries in each state exhibiting degraded or adverse levels of an indicator. Eutrophication, a condition of high nutrients often resulting in low oxygen levels and other adverse effects, is an important water quality concern for estuaries along the gulf coast. The National Oceanic and Atmospheric Administration (NOAA) has compared the Gulf of Mexico to other coastal regions like the middle Atlantic and has ranked the Gulf of Mexico as having the highest number of point sources of nutrients and the highest percentage of land use devoted to agriculture. We evaluated monitoring data for nitrogen, chlorophyll, and dissolved oxygen as indicators of eutrophication. Although most of the estuaries exhibited high nitrogen or chlorophyll or low dissolved oxygen concentrations at least once during a survey, many times these conditions were observed in small rivers or bayous rather than in the entire estuary. Often, the percent area affected was low. The gulf estuaries had moderate conditions overall for nutrients and dissolved oxygen. Definite nutrient problems were observed in >25% of the estuarine area in Louisiana and Texas and definite dissolved oxygen problems were observed in Alabama. Contaminants in estuarine sediments provide evidence of the accumulation of chemicals from anthropogenic sources. We compared the concentrations of sediment contaminants to established guideline values to determine the proportion of estuarine area that could have potential adverse effects on living organisms. Although detectable levels of contaminants were measured in almost every estuary in the Gulf of Mexico, <25% of the estuarine area in all states had contaminant concentrations that exceeded these guidelines. Wetlands are integral parts of estuarine systems. Declining acreage means habitat loss that may be the result of commercial and residential development, hydrologic alterations, or dredge and fill operations. The Gulf of Mexico region contains more than 50% of the coastal wetland acreage in the U.S. and yet it also has the highest rate of coastal wetland loss. Nine of the top ten estuarine drainage areas ranked by total wetland area are in the Gulf of Mexico region. The most current estimates of total wetland loss over the past 200 years range from 41% to 54% for the gulf states. Although coastal wetlands continue to be altered or destroyed, some estimates indicate that the rate of loss has slowed. All gulf states were rated as having severe problems with wetland loss. The condition of benthic (bottom-dwelling) invertebrates, fish and shellfish, birds, and threatened and endangered species was used to evaluate the health of estuarine fauna. Degraded benthic communities inhabited <25% of the estuarine area in all gulf states except for Texas. Commercial fish and shellfish landings may be used as an indicator of population stability while fish biomarkers are used to measure the health of individuals in the population. Commercial landings of the top four fisheries (shrimp, menhaden, blue crab, and oyster) are stable in the gulf states while fish biomarkers indicate fair to poor fish health in Alabama and Texas and good fish health elsewhere. Coastal and marine bird populations appear to be in good condition throughout the gulf. Four threatened or endangered species inhabit coastal areas in the Gulf of Mexico: brown pelican, Gulf sturgeon, manatee, and Kemp’s ridley sea turtle. In general, populations of these species are in good to fair condition in the gulf states. Public health indicators include shellfish bed closures and chemicals found in edible fish tissue. Harvest of shellfish (primarily oyster in the Gulf of Mexico) is restricted or prohibited when concentrations of bacteria or other pathogens reach levels that could impair human health. The gulf states contain the most acreage of shellfish-growing waters in the U.S. but also have the most acreage restricted for harvest. All gulf states except Mississippi have >25% of their shellfish-growing waters restricted for harvest, mostly due to pollution from wastewater treatment plants or other upstream sources. Advisories may be issued that limit consumption when the concentrations of chemicals in fish tissue exceed levels known to be harmful to humans. Although seafood consumption advisories have been issued in all gulf states, the percent of the fish population with high concentrations of contaminants is relatively low in the gulf overall.

Alabama, Florida, Louisiana, Mississippi, Texas↗

USGS1995

Water-quality assessment of the Rio Grande Valley study unit, Colorado, New Mexico, and Texas -- Analysis of selected nutrient, suspended-sediment, and pesticide data

This report contains a summary of data compiled from sources throughout the Rio Grande Valley study unit of the National Water-Quality Assessment program. Information presented includes the sources and types of water-quality data available, the utility of water-quality data for statistical analysis, and a description of recent water-quality conditions and trends and their relation to natural and human factors. Water-quality data are limited to concentrations of selected nutrient species in surface water and ground water, concentrations of suspended sediment and suspended solids in surface water, and pesticides in surface water, ground water, and biota. The Rio Grande Valley study unit includes about 45,900 square miles in Colorado, New Mexico, and Texas upstream from the streamflow-monitoring station Rio Grande at El Paso, Texas. The area also includes the San Luis Closed Basin and the surface-water closed basins east of the Continental Divide and north of the United States-Mexico international border. The Rio Grande drains about 29,300 square miles in these States; the remainder of the study unit area is in closed basins. Concentrations of all nutrients found in surface-water samples collected from the Rio Grande, with the exception of phosphorus, generally remained nearly constant from the northernmost station in the study unit to Rio Grande near Isleta, where concentrations were larger by an order of magnitude. Total nitrogen and total phosphorus loads increased downstream between Lobatos, Colorado, and Albuquerque, New Mexico. Nutrient concentrations remained elevated with slight variations until downstream from Elephant Butte Reservoir, where nutrient concentrations were lower. Nutrient concentrations then increased downstream from the reservoir, as evidenced by elevated concentrations at Rio Grande at El Paso, Texas. Suspended-sediment concentrations were similar at stations upstream from Otowi Bridge near San Ildefonso, New Mexico. The concentration and estimated load were nearly two orders of magnitude larger at this station relative to upstream stations. Cochiti Lake allows suspended sediment to settle, thus the resulting concentration is substantially lower downstream from the reservoir. Downstream from Cochiti Lake, concentrations again increased due to inflow from tributaries, other ephemeral streams and arroyos, and agricultural and urban areas. Two ephemeral tributaries (Rio Puerco and Rio Salado, which are south of Albuquerque) contribute substantial amounts of suspended sediment to the Rio Grande. Suspended-sediment concentrations in the Rio Grande just downstream from Elephant Butte Dam decreased by nearly three orders of magnitude due to settling in the reservoir. Concentrations then increased due to agricultural and urban impacts downstream from the reservoir. Nutrients in ground water in the study unit do not appear to be a widespread problem. However, localized areas that have elevated nitrate concentrations have been documented. The largest median nitrate concentration was found in water from wells located in the Basin and Range-mountains-urban data stratum (3.0 milligrams per liter) and the smallest median nitrate concentration was found in water from wells located in the Southern Rocky Mountainsmountains-forest data stratum (0.08 milligram per liter). Few (3 percent) nitrate concentrations in water from wells in all data strata were greater than 10 milligrams per liter, and most (82 percent) were less than 2 milligrams per liter. Comparison of nitrate concentrations in water from wells located in specific land-use settings across all hydrogeologic settings, with the exception of the Colorado Plateau, indicated that the largest median nitrate concentration was associated with rangeland land use and that larger nitrate concentrations were found in water from shallow wells. Water from wells located in areas of rangeland land use consistently had larger median nutrient concentrations than water from wells in areas of other land uses. The largest median ammonia concentration was in water from wells located in the Colorado Plateau-San Juan Basin-rangeland data stratum (0.27 milligram per liter). Most median ammonia concentrations were less than 0.03 milligram per liter, indicating that elevated ammonia concentrations are not a major issue in the study unit. The largest median orthophosphate concentration was found in water from wells located in the Southern Rocky Mountains-mountains-forest data stratum (0.15 milligram per liter) and the smallest was found in water from wells located in the Basin and Range-mountains-urban data stratum (0.02 milligram per liter). Most orthophosphate concentrations (85 percent) sampled were less than 0.2 milligram per liter, indicating that elevated orthophosphate concentrations are not a major issue in the study unit. Pesticide analyses were available for only 38 ground-water sampling sites in the Rio Grande Valley study unit. Diazinon, at a concentration of 0.01 microgram per liter, was the only pesticide detected and it was detected at only one site. More study is needed to determine if pesticides are affecting ground-water quality in the Rio Grande Valley study unit. Surface-water biological pesticide data were inadequate for in-depth analysis. The primary sources of data were the U.S. Fish and Wildlife Service and the U.S. Geological Survey. In the U.S. Fish and Wildlife Service study p,p'-DDE, a degradation product of DDT, was detected most frequently; highest concentrations were found at Stahman Farms in carp (6.3 micrograms per gram wet-weight) and at Hatch in Western kingbird (5.1 micrograms per gram wet-weight). In the U.S. Geological Survey study of Bosque del Apache National Wildlife Refuge no detectable organochlorine concentrations were found in plants, but detectable levels of p,p'-DDE were found in coot and carp, with a maximum concentration of 0.12 microgram per gram wet-weight found in coot.

Colorado, New Mexico, Texas↗

USGS2014

Aquifers of Arkansas: protection, management, and hydrologic and geochemical characteristics of groundwater resources in Arkansas

Sixteen aquifers in Arkansas that currently serve or have served as sources of water supply are described with respect to existing groundwater protection and management programs, geology, hydrologic characteristics, water use, water levels, deductive analysis, projections of hydrologic conditions, and water quality. State and Federal protection and management programs are described according to regulatory oversight, management strategies, and ambient groundwater-monitoring programs that currently (2013) are in place for assessing and protecting groundwater resources throughout the State. Physical attributes, groundwater geochemistry, and groundwater quality are described for each of the 16 aquifers of the State. Information in regard to the hydrology and geochemistry of each of the aquifers is summarized from about 550 historical and recent publications. Additionally, more than 8,000 sites with groundwater-quality data were obtained from the U.S. Geological Survey National Water Information System and the Arkansas Department of Environmental Quality databases and entered into a spatial database to investigate distribution and trends in chemical constituents for each of the aquifers. The 16 aquifers of the State were divided into two major physiographic regions of the State: the Coastal Plain Province (referred to as Coastal Plain) of eastern and southern Arkansas, which includes 11 of the 16 aquifers, and the Interior Highlands Division (referred to as Interior Highlands) of western Arkansas, which includes the remaining 5 aquifers. The 11 aquifers in the Coastal Plain consist of various geologic units that are Cenozoic in age and consist primarily of Cretaceous, Tertiary, and Quaternary sands, gravels, silts, and clays. Groundwater in the Coastal Plain represents one of the most valuable natural resources in the State, driving the economic engines of agriculture, while also supplying abundant water for commercial, industrial, and public-supply use. In terms of age from youngest to oldest, the aquifers of the Coastal Plain include Quaternary alluvial aquifers, including the Mississippi River Valley alluvial aquifer (the most important aquifer in Arkansas in terms of volume of use and economic benefits), the Jackson Group (a regional confining unit that served for decades as an important source of domestic supply), and the Cockfield, Sparta, Cane River, Carrizo, Wilcox, Nacatoch, Ozan, Tokio, and Trinity aquifers. The Mississippi River Valley alluvial aquifer accounts for approximately 94 percent of all groundwater used in the State, and the aquifer is used primarily for irrigation purposes. The Sparta aquifer is the second most important aquifer in terms of use, and the aquifer was used in the past dominantly as a source of public and industrial supply, although increasing irrigation use is occurring because of critically declining water levels in the Mississippi River Valley alluvial aquifer. Other aquifers of the Coastal Plain generally are used as important local sources of domestic, industrial, and public supply, in addition to other minor uses. Water quality generally is good for all aquifers of the Coastal Plain, except for elevated iron concentrations and localized areas of high salinity. The high salinity results from intrusion from underlying formations, evapotranspiration processes in areas of low recharge, and inadequate flushing in downgradient areas of residual salinity from deposition in marine environments. Trends in the spatial distribution of individual chemical constituents are related to position along the flow path for most aquifers of the Coastal Plain. These trends include elevated iron and nitrate concentrations with lower pH values and dissolved solids in groundwater from the outcrop areas, transitioning to lower iron and nitrate (related to changes in redox) and higher pH and dissolved solids (dominantly from the dissolution of carbonate minerals) in groundwater downgradient from outcrop areas. Groundwater generally trended from a calcium- to a sodium-bicarbonate water type with increasing cation exchange along the flow path. The Interior Highlands of western Arkansas has less reported groundwater use than other areas of the State, reflecting a combination of factors. These factors include prevalent and increasing use of surface water, less intensive agricultural uses, lower population and industry densities, lesser potential yield of the resource, and lack of detailed reporting. The overall low yields of aquifers of the Interior Highlands result in domestic supply as the dominant use, with minor industrial, public, and commercial-supply use. Where greater volumes are required for growth of population and industry, surface water is the greatest supplier of water needs in the Interior Highlands. The various aquifers of the Interior Highlands generally occur in shallow, fractured, well-indurated, structurally modified bedrock of this mountainous region of the State, as compared to the relatively flat-lying, unconsolidated sediments of the Coastal Plain. In terms of age from youngest to oldest, the aquifers of the Interior Highlands include: the Arkansas River Valley alluvial aquifer, the Ouachita Mountains aquifer, the Western Interior Plains confining system, the Springfield Plateau aquifer, and the Ozark aquifer. Spatial trends in groundwater geochemistry in the Interior Highlands differ greatly from trends noted for aquifers of the Coastal Plain. In the Coastal Plain, the prevalence of long regional flow paths results in regionally predictable and mappable geochemical changes along the flow paths. In the Interior Highlands, short, topographically controlled flow paths (from hilltops to valleys) within small watersheds represent the predominant groundwater-flow system. As such, dense data coverage from numerous wells would be required to effectively characterize these groundwater basins and define small-scale geochemical changes along any given flow path for aquifers of the Interior Highlands. Changes in geochemistry generally were related to rock type and residence time along individual flow paths. Dominant changes in geochemistry for the Ouachita Mountains aquifer and the Western Interior Plains confining system are attributed to rock/water interaction and changes in redox zonation along the flow path. In these areas, groundwater evolves along flow paths from a calcium- to a sodium-bicarbonate water type with increasing reducing conditions resulting in denitrification, elevated iron and manganese concentrations, and production of methane in the more geochemically evolved and strongest reducing conditions. In the Ozark and Springfield Plateau aquifers, rapid influx of surface-derived contaminants, especially nitrogen, coupled with few to no attenuation processes was attributed to the karst landscape developed on Mississippian- and Ordovician-age carbonate rocks of the Ozark Plateaus. Increasing nitrate concentrations are related to increasing agricultural land use, and areas of mature karst development result in higher nitrate concentrations than areas with less karst features.

Arkasas↗

USGS2007

Hydrogeology, Ground-Water-Age Dating, Water Quality, and Vulnerability of Ground Water to Contamination in a Part of the Whitewater Valley Aquifer System near Richmond, Indiana, 2002-2003

Assessments of the vulnerability to contamination of ground-water sources used by public-water systems, as mandated by the Federal Safe Drinking Water Act Amendments of 1996, commonly have involved qualitative evaluations based on existing information on the geologic and hydrologic setting. The U.S. Geological Survey National Water-Quality Assessment Program has identified ground-water-age dating; detailed water-quality analyses of nitrate, pesticides, trace elements, and wastewater-related organic compounds; and assessed natural processes that affect those constituents as potential, unique improvements to existing methods of qualitative vulnerability assessment. To evaluate the improvement from use of these methods, in 2002 and 2003, the U.S. Geological Survey, in cooperation with the City of Richmond, Indiana, compiled and interpreted hydrogeologic data and chemical analyses of water samples from seven wells in a part of the Whitewater Valley aquifer system in a former glacial valley near Richmond. This study investigated the application of ground-water-age dating, dissolved-gas analyses, and detailed water-quality analyses to quantitatively evaluate the vulnerability of ground water to contamination and to identify processes that affect the vulnerability to specific contaminants in an area of post-1972 greenfield development. The aquifer system in the study area includes an unconfined sand and gravel aquifer used for public-water supply (upper aquifer) and a confined sand and gravel aquifer (lower aquifer) separated by a till confining unit. Several hydrogeologic and cultural measures indicate that the upper aquifer is qualitatively vulnerable to contamination: the upper aquifer is unconfined and has a shallow depth to the water table (from about 4.75 to 14 feet below land surface), low-permeability sediments in the unsaturated zone are thin (less than 10 feet thick), estimated ground-water-flow rates through the upper aquifer are relatively rapid (the highest estimated rates ranged from 0.44 to about 5.0 feet per day), and potential contaminant sources were present. Ground-water-age dates indicate that ground-water samples represented recharge from about the time greenfield development began south of the ground-water-flow divide and that changes in water quality would lag changes in contaminant inputs. Estimates of ground-water age, computed with dichlorodifluoromethane (CFC-12) and trichlorotrifluoroethane (CFC-113) concentrations in water samples collected from seven observation wells in February and March 2003, indicated that water in the upper aquifer had recharged within about 13 to 30 years before sampling. Ground-water ages were youngest (from about 13 to 15 years since recharge) in water from the shallow wells along the glacial-valley margin and oldest (30 years) in water from a well at the base of the aquifer in the valley center. Ground-water ages determined for the shallow wells may be affected by mixing of recent recharge with older ground water from deeper in the aquifer, as indicated by upward hydraulic gradients between paired shallow and deep wells in the upper aquifer. Other parts of the Whitewater Valley aquifer system with similar hydrogeologic characteristics could be expected to have similarly young ground-water ages and residence times. Analyses of water samples collected from the seven observation wells in August and September 2002 indicated that concentrations of chloride, sodium, and nitrate generally were larger in ground water from the upper aquifer than in other parts of the Whitewater Valley aquifer system. Drinking-water-quality standards for Indiana were exceeded in water samples from one well for chloride concentrations, from four wells for dissolved-solids concentrations, and from one well for nitrate concentrations. Application of low-level methods for trace-element analyses determined that concentrations of aluminum, cobalt, iron, lithium, molybdenum, nickel, selenium, uranium, vanadium, and zinc were less than or equal to 8 micrograms per liter; concentrations of arsenic, cadmium, chromium, and copper were less than or equal to 1 microgram per liter. Application of low-level analytical methods to water samples enabled the detection of several pesticides and volatile, semivolatile, and wastewater-related organic compounds; concentrations of individual pesticides and volatile organic compounds were less than 0.1 microgram per liter and concentrations of individual wastewater organic compounds were less than 0.5 microgram per liter. The low-level analytical methods will provide useful data with which to compare future changes in water quality. Results of detailed water-quality analyses, ground-waterage dating, and dissolved-gas analyses indicated the vulnerability of ground water to specific types of contamination, the sequence of contaminant introduction to the aquifer relative to greenfield development, and processes that may mitigate the contamination. Concentrations of chloride and sodium and chloride/bromide weight ratios in sampled water from five wells indicated the vulnerability of the upper aquifer to roaddeicer contamination. Ground-water-age estimates from these wells indicated the onset of upgradient road-deicer use within the previous 25 years. Nitrate in the upper aquifer predates the post-1972 development, based on a ground-water-age date (30 years) and the nitrate concentration (5.12 milligrams per liter as nitrogen) in water from a deep well. Vulnerability of the aquifer to nitrate contamination is limited partially by denitrification. Detection of one to four atrazine transformation products in water samples from the upper aquifer indicated biological and hydrochemical processes that may limit the vulnerability of the ground water to atrazine contamination. Microbial processes also may limit the aquifer vulnerability to small inputs of halogenated aliphatic compounds, as indicated by microbial transformations of trichlorofluoromethane and trichlorotrifluoroethane relative to dichlorodifluoromethane. The vulnerability of ground water to contamination in other parts of the aquifer system also may be mitigated by hydrodynamic dispersion and biologically mediated transformations of nitrate, pesticides, and some organic compounds. Identification of the sequence of contamination and processes affecting the vulnerability of ground water to contamination would have been unlikely with conventional assessment methods.

Indiana, Ohio↗

USGS2007

Evaluation of ground-water and boron sources by use of boron stable-isotope ratios, tritium, and selected water-chemistry constituents near Beverly Shores, northwestern Indiana, 2004

Concentrations of boron greater than the U.S. Environmental Protection Agency (USEPA) 900 μg/L removal action level (RAL) standard were detected in water sampled by the USEPA in 2004 from three domestic wells near Beverly Shores, Indiana. The RAL regulates only human-affected concentrations of a constituent. A lack of well logs and screened depth information precluded identification of whether water from sampled wells, and their boron sources, were from human-affected or natural sources in the surficial aquifer, or associated with a previously defined natural, confined aquifer source of boron from the subtill or basal sand aquifers. A geochemically-based classification of the source of boron in ground water could potentially determine the similarity of boron to known sources or mixtures between known sources, or classify whether the relative age of the ground water predated the potential sources of contamination. The U.S. Geological Survey (USGS), in cooperation with the USEPA, investigated the use of a geochemical method that applied boron stable isotopes, and concentrations of boron, tritium, and other constituents to distinguish between natural and human-affected sources of boron in ground water and thereby determine if the RAL was applicable to the situation. Boron stable-isotope ratios and concentrations of boron in 17 ground-water samples and tritium concentrations in 9 ground-water samples collected in 2004 were used to identify geochemical differences between potential sources of boron in ground water near Beverly Shores, Indiana. Boron and δ 11 B analyses for this investigation were made on unacidified samples to assure consistency of the result with unacidified analyses of δ 11 B values from other investigations. Potential sources of boron included surficial-aquifer water affected by coal-combustion products (CCP) or domestic-wastewater, upward discharge of ground water from confined aquifers, and unaffected water from the surficial aquifer that was distant from human-affected boron sources. Boron concentrations in potential ground-water sources of boron were largest (15,700 to 24,400 μg/L) in samples of CCP-affected surficial aquifer water from four wells at a CCP landfill and smallest (27 to 63 μg/L) in three wells in the surficial aquifer that were distant from human-affected boron sources. Boron concentrations in water from the basal sand aquifer ranged from 656 μg/L to 1,800 μg/L. Boron concentrations in water from three domestic-wastewater-affected surficial aquifer wells ranged from 84 to 387 μg/L. Among the representative ground-water samples, boron concentrations from all four samples of CCP-affected surficial aquifer water and four of five samples of water from the basal sand aquifer had concentrations greater than the RAL. A comparison of boron concentrations in acid-preserved and unacidified samples indicated that boron concentrations reported for this investigation may be from about 11 to 16 percent less than would be reported in a standard analysis of an acidified sample. The stable isotope boron-11 was most enriched in comparison to boron-10 in ground water from a confined aquifer, the basal sand aquifer (δ 11 B, 24.6 to 34.0 per mil, five samples); it was most depleted in CCP-affected water from the surficial aquifer (δ 11 B, 0.1 to 6.6 per mil, four samples). Domestic-wastewater-affected water from the surficial aquifer (δ 11 B, 8.7 to 11.7 per mil, four samples) was enriched in boron-11, in comparison to individual samples of a borax detergent additive and a detergent with perborate bleach; it was intermediate in composition between basal sand aquifer water and CCP-affected water from the surficial aquifer. The similarity between a ground-water sample from the surficial aquifer and a hypothetical mixture of unaffected surficial aquifer and basal sand aquifer waters indicates the potential for long-term upward discharge of ground water into the surficial aquifer from one or more confined aquifers. Estimated δ 11 B values for acidified samples were depleted by 1.9 to 2.8 per mil in comparison to unacidified samples from the four wells sampled; those differences were small in comparison to the differences between δ 11 B values of representative sources of boron in ground water. Tritium concentrations ranged from 7.0 to 10.3 tritium units in six samples from the surficial aquifer and were less than 0.8 tritium units in three samples from the basal sand aquifer. Water from wells in the surficial aquifer represents predominantly modern, post-1972 recharge and sources of boron and other constituents. Water from the basal sand aquifer is associated with pre-1952 recharge from sources not affected by local boron inputs. Ground water from six wells (five domestic wells and one public-supply well) where the ground-water source was unknown had boron concentrations, boron isotope ratios, and tritium concentrations similar to water from the basal sand aquifer. Boron concentrations greater than the RAL were found in water from four of these six wells. The boron isotope and tritium data from these four wells indicate a natural source of boron in ground water; therefore, the RAL does not apply to boron concentrations in water from these wells. Water samples from two domestic wells where the ground-water source was unknown had boron concentrations less than the RAL and boron isotope ratios and tritium concentrations that were similar to domestic-wastewater-affected water from the surficial aquifer. The boron isotope ratio for a sample from one domestic well was similar to that of CCP-affected water from the surficial aquifer and detergent compositions; the boron concentration of that sample was less than the RAL. The classifications of differences among representative sources of boron in ground water and water samples from wells where the ground-water source was unknown generally agreed with distinctions based on strontium-87/strontium-86 ratios and concentrations of strontium, chloride, nitrate, and ammonia. This application of boron concentrations, boron isotope ratios, and tritium concentrations to classify differences in relation to potential sources of boron in ground water was able to distinguish between boron from natural sources and from human-affected sources that are subject to regulation.

Indiana↗

USGS2022

Fishway Entrance Palisade

This technical report summarizes the work that was conducted by the University of Massachusetts Amherst and the United States Geological Survey (USGS), along with other project partners, on the Fishway Entrance Palisade (EP), a projected funded through the Department of Energy’s (DOE) funding opportunity titled ‘Innovative Solutions for Fish Passage at Hydropower Dams’ (DE‐FOA‐0001662). The period of performance ranged from September 1, 2018 through September 30, 2021. The EP is a novel fish passage engineering technology designed to provide more favorable entry conditions for fish and to reduce costs relative to conventional fishway auxiliary water systems (AWS). The EP project has four primary components. First, the Northeast United States Auxiliary Water Systems Database was created (Northeast Fishway Auxiliary Water Systems Database Section). The database, developed with material provided by the U.S. Fish and Wildlife Service, contains information on fishway type (e.g., lift, Denil, pool and weir) and Auxiliary Water System (AWS) details (e.g., water conveyance method, diffuser type) for 60 hydroelectric sites in the region. Findings indicate that nearly 4 out of every 10 fishway in the region is a fish lift and approximately 1 out of every 4 is a Denil ladder. The remainder are a mix of vertical slot fishways, pool and weirs, and Ice Harbor fishways. Furthermore, over half of all AWS systems use floor diffusers to discharge the auxiliary (or attraction) water into the entrance of a fishway, whereas only 14% use wall diffusers. Second, limited experiments on a conventional AWS with live, actively migrating fish were conducted at the USGS Easter Ecological Science Center (EESC) S.O. Conte Research Laboratory (Conventional Auxiliary Water System Experiments Section). This study determined how water velocity through a wall diffuser, without turning vanes or timber baffles to distribute the flow, affects the behavior and passage of adult American shad, a conservative surrogate species for migratory fish on the East Coast. Two gross diffuser velocity treatments were examined, 0.5 ft/s and 1.0 ft/s. These wall diffuser velocities represented current (0.5 ft/s) and past (1.0 ft/s) design criteria guidelines set forth by the USFWS North Atlantic-Appalachian Region (Rojas 2020; USFWS 2019). Six trials with a total of 151 American Shad were conducted in June of 2019 for the two treatments. No differences in American shad passage efficiency were discovered between the two treatments, while approximately 3 in every 4 attempts were successful at passing the diffuser. While these results may appear to indicate that the generally accepted gross wall diffuser velocity criteria for American shad of 0.5 ft/s could be safely increased to 1.0 ft/s, further analysis is warranted. Furthermore, it is unknown how other migratory and resident fish species that traverse these structures would be impacted by such a change. Studying the wall diffuser hydraulics led to an important AWS observation. Without turning vanes or timber baffles in this study, doubling the diffuser area was insufficient at producing the type of flow field change one may expect by halving the gross diffuser velocity. Instead, the flow fields throughout each treatments study area were similar, which led to similar results in shad performance. This not only highlights the importance of installing flow guidance devices like turning vanes, but also to the importance of properly maintaining them, which can be costly. Third, more expansive experiments on the novel EP were conducted in the spring of 2019 and 2021 (Fishway Entrance Palisade Experiments). The goal of this study was to determine how adult American shad responded to a variety of conditions at a full-scale EP. A total of six treatments were examined by changing the average auxiliary channel velocity between 1.0 and 5.0 ft/s in intervals of 1.0 ft/s and by inserting/removing an entrance gate at the opening of the fishway. Thirty trials with a total of 1,273 shad were conducted over the two years. In all treatments, at least ~7 out of every 10 fish successfully passed the EP diffuser and swam into the entrance channel within the 3.5-hour long trial, highlighting the general effectiveness of the novel AWS technology. In both study years, lower velocities through the EP diffuser led to increased shad performance, though performance peaked for the 2 ft/s velocity treatment. This treatment condition represents an approximate six-fold increase in gross diffuser velocity relative to conventional auxiliary water systems, which in turn presents opportunities for cost savings (e.g., reduction in diffuser size). Shad performance, in general, was worse in 2019 than in 2021, potentially due to the different run timing when our trials were conducted (2019 trials occurred near the end of the migration season, unlike in 2021). Treatments in 2019 had approximately a 20% reduction in entrance efficiency by the trial end, including a 16.7% drop for the 3 ft/s velocity treatment in 2019 relative to 2021 (the only carryover treatment between years). Lastly, adding an entrance gate caused a significant delay to entry. The time to 25% entry raised ~20 minutes from the near instantaneous 25% entry that was reported for the other treatments conducted in the same year (2021). Though by the end of the 3.5-hour trial, the overall entrance efficiency nearly matched those of the other 2021 treatments. The fourth and final component of the EP project was an economic analysis that focused on the cost of attraction and environmental flows (Modeling Power Generation Losses Due to Environmental and Fish Passage Attraction Flows at a Run-Of-River Hydroelectric Operation in the Northeast). The study assessed the economic impact of meeting environmental flow requirements at a representative hydroelectric facility and fish lift in the Northeast. An initial finding of the study was that there is a paucity of published data on the costs of meeting attraction and environmental flows. This is due, in part, to the proprietary nature of this data. To explore the costs associated with these flows, three types of environmental flows were assessed: upstream fishway attraction flows, downstream fishway attraction flows, and habitat maintenance minimum flows. A physics-based model was developed and calibrated with three years of hourly generation and flow data as inputs. Gage flow inputs were adjusted and used to calculate power generated. To address hydrologic variability, the model was executed to simulate 30 years of historical flows. Results indicate that both interannual and seasonal climatic factors impact the costs of meeting environmental flow requirements. Generation potential is most strongly curtailed during dry years in terms of maximizing the capacity factor (the percent of time a plant generates at capacity). Dry years, and especially dry summers, have the most significant costs associated with mitigation flows. Of the three types of flows, habitat flows are most costly in terms of power production, followed by upstream attraction flows. Downstream attraction flows are least costly. This finding is the likely result of differences in both flow rates and duration of the seasonal requirement for each flow. Overall, environmental flows represented a 2-12% loss in annual generation, but losses during a dry summer can reach over 20%.

Final Technical Report↗

USGS2025

Calibration of the Stream Salmonid Simulator (S3) model to estimate annual survival, movement, and food consumption by juvenile Chinook salmon (Oncorhynchus tshawytscha) in the restoration reach of the Trinity River, California, 2006–18

Executive Summary The Trinity River is managed in two sections: (1) from the upper 64-kilometer “restoration reach” downstream from Lewiston Dam to the confluence with the North Fork Trinity River, and (2) the 120-kilometer lower Trinity River downstream from the restoration reach. The Stream Salmonid Simulator (S3) has been previously applied to these reaches and the Klamath River. To estimate fish growth, past S3 calibration efforts in the Trinity and Klamath Rivers used maximum likelihood methods that considered only the abundance of juvenile Chinook salmon ( Oncorhynchus tshawytscha ) passing a fish trap to estimate survival and movement parameters, but not fish consumption. Previous calibrations did not estimate the average proportion of maximum consumption ( C y ) when estimating survival ( S y ) and movement ( M 0 y ) parameters across years ( y ) of data, but because no other information was available in the literature a fixed value of C y =0.66 was assumed. Therefore, the goal of this report is to present an alternative approach that calibrates the S3 model to multivariate data (that is, abundance and size), enabling the estimation of the average proportion of maximum consumption, in conjunction with survival and movement parameters for a particular migration year. We fit the S3 model to individual years of weekly trap abundance estimates and mean fish sizes (fork length) at the Pear Tree Gulch (hereafter referred to as Pear Tree) fish trap representing the restoration reach. We used the Earth Mover’s Distance (EMD) as the objective value to be minimized in parameter optimization. This approach estimated survival, movement, and consumption parameters for each migration year. Because we had information on the abundance of natural and hatchery produced juvenile salmon at the fish traps, we estimated survival and movement for natural and hatchery fish. S3 is a deterministic life-stage-structured population model that tracks daily growth, movement, and survival of juvenile Chinook Salmon. A key theme of the model is that river discharge affects habitat availability and capacity, which in turn drives density-dependent population dynamics. To explicitly link population dynamics to habitat quality and quantity, the river environment is constructed as a one-dimensional series of linked habitat units, each of which has an associated daily timeseries of discharge, water temperature, and useable habitat area or carrying capacity. In turn, the physical characteristics of each habitat unit and the number of fish occupying each unit drive survival and growth within each habitat unit and movement of fish among habitat units. The physical template of the restoration reach of the Trinity River was classified into 356 meso-habitat units comprised of runs, riffles, and pools. For each habitat unit, we developed a timeseries of daily discharge, water temperature, amount of available spawning habitat, and fry and parr carrying capacity. Capacity time series were constructed using state-of-the-art models of spatially explicit hydrodynamics and quantitative fish habitat relationships developed for the Trinity River. These variables were then used to drive population dynamics such as egg maturation and survival, and in turn, juvenile movement, growth, and survival. We estimated movement, survival, and consumption parameters by calibrating the model to 12 years of weekly juvenile abundance estimates and fish sizes at the Pear Tree fish trap near the downstream end of the restoration reach. We estimated parameters for 12 years that included a wide range of female spawner abundances (1,414–11,494) and water year types (critically dry–extremely wet). We contrast the estimated parameters to the corresponding number of female spawners and the total annual volume of water discharged for the Trinity River (Trinity River Restoration Program; https://www.trrp.net/restoration/flows/summary/ ). The calibration consisted of replicating historical conditions as closely as possible (for example, discharge; temperature; spawner abundance, spawning location and timing, and hatchery releases), and then running the model to predict weekly abundance passing the trap location from each brood year of adults and subsequent migration year of their juvenile progeny. Because density-dependent movement was favored in past evaluations, we estimated S3 parameters based on density-independent survival and density-dependent movement. Likewise, each year’s estimated survival parameter for natural ( S N y ) and hatchery ( S H y ) fish may be interpreted as the mean daily survival probability from emergence or hatchery release to the Pear Tree fish trap. Under density dependence, the estimated movement parameter for natural ( M 0N y ) and hatchery ( M 0H y ) fish represents the intercept of the Beverton-Holt model; the probability of remaining in a habitat at near-zero abundance. We estimated C y by using EMD and incorporating abundance and fish size into model calibration. Average daily proportions of maximum consumption, , across the years were generally high (=0.640; standard deviation (SD) SD=0.176), suggesting that fish were feeding at about two-thirds of expected maximum consumption rates. This average proportion of maximum consumption,is very similar to what has been assumed (=0.66) in previous Trinity and Klamath River S3 calibration and simulation efforts. In 2017, we estimated the lowest C y , suggesting lower average consumption for juvenile salmon in high-discharge water years. When this high discharge year was excluded, there was no apparent trend in C y with annual water volume. Estimates of survival showed little trend over the range in spawner abundances, but a trend towards higher natural and hatchery fish survival with higher annual volumes of water was apparent. Over the 12 years, the average survival of hatchery fish was =0.888 (SD=0.079) and the average survival natural fish was=0.969 (SD=0.01). With respect to fish movement, we estimated higher M 0N y and M 0H y with higher annual volumes of water in the Trinity River. Higher M N0 y or M H0 y suggest greater probability of remaining in a habitat at low fish densities, with potential for density-dependent processes in movement to occur. The highest M 0N y = 0.676 was estimated during brood year 2012, and the overall average for natural fish was =0.276 (SD=0.188) and for hatchery fish was=0.467 (SD=0.235). Under the Beverton-Holt model, as M 0N y or M 0H y approach zero, there is less capacity for change in fish movement as fish density increases. The S3 model was initialized with only the spatiotemporal distribution of spawners, so it performed well at capturing the essential outmigration features that are ultimately governed by rates of growth, movement, and mortality. We used a new optimization method that could accommodate multivariate data on abundance and fish size collected at the Pear Tree fish trap, enabling the calibration of S3 to estimate five parameters for 12 separate years of data. Incorporating weekly fish size data for each year in our parameter optimization process made the estimation of C y possible and represents a step forward in the fitting of the S3 model to fish trap data for the purposes of parameter calibration and the estimation of growth parameters with respect to annual conditions. We identified lack of fit and adding important effects into the S3 model may improve the S3 estimation and simulation of water scenarios. The Trinity River Restoration Program (TRRP) Science Advisory Board recommended that the TRRP focus on developing core elements of a decision support system (DSS; Buffington and others, 2014). Toward that end, the habitat and S3 models described in this report are both core elements of the DSS. The structure of S3 makes it a particularly useful fish production model for the DSS because population dynamics are sensitive to (1) water temperature, (2) daily discharge management, and (3) habitat quality and quantity. Each of these variables are key management parameters under consideration in the TRRP. As such, the S3 model may provide valuable insights into the potentially variable effects of different management decisions on the Trinity River.

California↗

USGS2013

Sources and characteristics of organic matter in the Clackamas River, Oregon, related to the formation of disinfection by-products in treated drinking water

This study characterized the amount and quality of organic matter in the Clackamas River, Oregon, to gain an understanding of sources that contribute to the formation of chlorinated and brominated disinfection by-products (DBPs), focusing on regulated DBPs in treated drinking water from two direct-filtration treatment plants that together serve approximately 100,000 customers. The central hypothesis guiding this study was that natural organic matter leaching out of the forested watershed, in-stream growth of benthic algae, and phytoplankton blooms in the reservoirs contribute different and varying proportions of organic carbon to the river. Differences in the amount and composition of carbon derived from each source affects the types and concentrations of DBP precursors entering the treatment plants and, as a result, yield varying DBP concentrations and species in finished water. The two classes of DBPs analyzed in this study-trihalomethanes (THMs) and haloacetic acids (HAAs)-form from precursors within the dissolved and particulate pools of organic matter present in source water. The five principal objectives of the study were to (1) describe the seasonal quantity and character of organic matter in the Clackamas River; (2) relate the amount and composition of organic matter to the formation of DBPs; (3) evaluate sources of DBP precursors in the watershed; (4) assess the use of optical measurements, including in-situ fluorescence, for estimating dissolved organic carbon (DOC) concentrations and DBP formation; and (5) assess the removal of DBP precursors during treatment by conducting treatability "jar-test" experiments at one of the treatment plants. Data collection consisted of (1) monthly sampling of source and finished water at two drinking-water treatment plants; (2) event-based sampling in the mainstem, tributaries, and North Fork Reservoir; and (3) in-situ continuous monitoring of fluorescent dissolved organic matter (FDOM), turbidity, chlorophyll- a , and other constituents to continuously track source-water conditions in near real-time. Treatability tests were conducted during the four event-based surveys to determine the effectiveness of coagulant and powdered activated carbon (PAC) on the removal of DBP precursors. Sample analyses included DOC, total particulate carbon (TPC), total and dissolved nutrients, absorbance and fluorescence spectroscopy, and, for regulated DBPs, concentrations of THMs and HAAs in finished water and laboratory-based THM and HAA formation potentials (THMFP and HAAFP, respectively) for source water and selected locations throughout the watershed. The results of this study may not be typical given the record and near record amounts of precipitation that occurred during spring that produced streamflow much higher than average in 2010-11. Although there were algal blooms, lower concentrations of chlorophyll- a were observed in the water column during the study period compared to historical data. Concentrations of DBPs in finished (treated) water averaged 0.024 milligrams per liter (mg/L) for THMs and 0.022 mg/L for HAAs; maximum values were about 0.040 mg/L for both classes of DBPs. Although DBP concentrations were somewhat higher within the distribution system, none of the samples collected for this study or for the quarterly compliance monitoring by the water utilities exceeded levels permissible under existing U.S. Environmental Protection Agency (USEPA) regulations: 0.080 mg/L for THMs and 0.060 mg/L for HAAs. DOC concentrations were generally low in the Clackamas River, typically about 1.0-1.5 mg/L. Concentrations in the mainstem occasionally increased to nearly 2.5 mg/L during storms; DOC concentrations in tributaries were sometimes much higher (up to 7.8 mg/L). The continuous in-situ FDOM measurements indicated sharp rises in DOC concentrations in the mainstem following rainfall events; concentrations were relatively stable during summer base flow. Even though the first autumn storm mobilized appreciable quantities of carbon, higher concentrations of DBPs in finished water were observed 3-weeks later, after the ground was saturated from additional rainfall. The majority of the DOC in the lower Clackamas River appears to originate from the upper basin, suggesting terrestrial carbon was commonly the dominant source. Lower-basin tributaries typically contained the highest concentrations of DOC and DBP precursors and contributed substantially to the overall loads in the mainstem during storms. During low-flow periods, tributaries were not major sources of DOC or DBP precursors to the Clackamas River. Although the dissolved fraction of organic carbon contributed the majority of DBP precursors, at times the particulate fraction (inorganic sediment and organic particles including detritus and algal material) contributed a substantial fraction of DBP precursors. Considering just the main-stem sites, on average, 10 percent of THMFP and 32 percent of HAAFP were attributed to particulate carbon. This finding suggests water-treatment methods that remove particles prior to chlorination would reduce finished-water DBP concentrations to some degree. Overall, concentrations of THM and HAA precursors were closely linked to DOC concentrations; laboratory DBP formation potentials (DBPFPs) clearly showed that THMFP and HAAFP were greatest in the downstream tributaries that contained elevated carbon concentrations. However, carbon-normalized "specific" formation potentials for THMs and HAAs (STHMFP and SHAAFP, respectively) revealed changes in carbon character over time that affected the two types of DBP classes differently. HAA precursors were elevated in waters containing aromatic-rich soil-derived material arising from forested areas. In contrast, THM precursors were associated with carbon having a lower aromatic content; highest STHMFP occurred in autumn 2011 in the mainstem from North Fork Reservoir downstream to LO DWTP. This pattern suggests the potential for a link between THM precursors and algal-derived carbon. The highest STHMFP value was measured within North Fork Reservoir, indicating reservoir derived carbon may be important for this class of DBPs. Weak correlations between STHMFP and SHAAFP emphasize that precursor sources for these types of DBPs may be different. This highlights not only that different locations within the watershed produce carbon with different reactivity (specific DBPFP), but also that different management approaches for each class of DBP precursors could be required for control. Treatability tests conducted on source water during four basin-wide surveys demonstrated that an average of about 40 percent of DOC can be removed by coagulation. While the decrease in THMFP following coagulation was similar to DOC, the decrease in HAAFP was much greater (approximately 70 percent), indicating coagulation is particularly effective at removing HAA precursors'likely because of the aromatic nature of the carbon associated with HAA precursors. Several findings from this study have direct implications for managing drinking-water resources and for providing useful information that may help improve treatment-plant operations. For example, the use of in-situ fluorometers that measure FDOM provided an excellent proxy for DOC concentration in this system and revealed short-term, rapid changes in DOC concentration during storm events. In addition, the strong correlation between FDOM values measured in-situ and HAA5 concentrations in finished water may permit estimation of continuous HAA concentrations, as was done here. As part of this study, multiple in-situ FDOM sensors were deployed continuously and in real-time to characterize the composition of dissolved organic matter. Although the initial results were promising, additional research and engineering developments will be needed to demonstrate the full utility of these sensors for this purpose. In conclusion, although DBPFPs were strongly correlated to DOC concentration, some DBPs formed from particulate carbon, including terrestrial leaf material and algal material such as planktonic species of blue-green algae and sloughed filaments, stalks, and cells of benthic algae. Different precursor sources in the watershed were evident from the data, suggesting specific actions may be available to address some of these sources. In-situ measurements of FDOM proved to be an excellent proxy for DOC concentration as well as HAA formation during treatment, which suggests further development and refinement of these sensors have the potential to provide real-time information about complex watershed processes to operators at the drinking-water treatment plants. Follow-up studies could examine the relative roles that terrestrial and algal sources have on the DBP precursor pool to better understand how watershed-management activities may be affecting the transport of these compounds to Clackamas River drinking-water intakes. Given the low concentrations of algae in the water column during this study, additional surveys during more typical river conditions could provide a more complete understanding of how algae contribute DBP precursors. Further development of FDOM-sensor technology can improve our understanding of carbon dynamics in the river and how concentrations may be trending over time. This study was conducted in collaboration with Clackamas River Water and the City of Lake Oswego water utilities. Other research partners included Oregon Health and Science University in Hillsboro, Oregon, Alexin Laboratory in Tigard, Oregon, U.S. Geological Survey National Research Program Laboratory in Denver, Colorado, and the U.S. Geological Survey Water Science Centers in Portland, Oregon, and Sacramento, California. This project was supported with funding from Clackamas River Water, City of Lake Oswego, the U.S. Geological Survey, and the Water Research Foundation.

Oregon↗

USGS2023

Least Bell's Vireos and Southwestern Willow Flycatchers at the San Luis Rey Flood Risk Management Project Area in San Diego County, California—Breeding activities and habitat use—2022 annual report

Executive Summary We completed four protocol surveys for Least Bell’s Vireos ( Vireo bellii pusillus ; vireo) during the breeding season, supplemented by weekly territory monitoring visits. We identified a total of 133 territorial male vireos; 114 were confirmed as paired, and 3 were confirmed as single males. For the remaining 16 territories, we were unable to confirm breeding status. Two transient vireos were detected in 2022. The vireo population in the Project Area increased by 9 percent from 2021 to 2022. The vireo population at Marine Corps Base Camp Pendleton also increased (4 percent), whereas the population at Marine Corps Air Station remained relatively stable (decreased from 10 pairs to 9) and the Otay River population decreased by 10 percent (2 territories). We used an index of treatment (Treatment Index) to evaluate the effect of on-going vegetation clearing on the Project Area vireo population. The Treatment Index measures the cumulative effect of vegetation treatment within a territory (since 2005) by using the percentage area treated weighted by the number of years since treatment. We determined that the Treatment Index for unoccupied habitat was more than four times that of occupied habitat, indicating that vireos selected habitat that was less treated in which to settle. We monitored vireo nests at three general site types: (1) within the flood channel where exotic and native vegetation removal has occurred regularly (Channel), (2) three sites near the flood channel where limited exotic and native vegetation removal has occurred (Off-channel), and (3) three sites that have been actively restored by planting native vegetation (Restoration). Nesting activity was monitored in 80 territories, 3 of which were occupied by single males and 1 by a male whose breeding status could not be confirmed. Overall, 38 percent of completed nests were successful and nest success did not differ among the three sites. In 2022, there were no differences with regard to clutch size, hatching, or fledging success among Channel, Off-channel and Restoration sites. Overall breeding success and productivity were slightly higher in 2022 than in 2021, with 72 percent of pairs fledgling at least one young and pairs fledging an average of 2.2±1.7 young. To investigate if the cumulative years of treatment had an effect on vireo reproductive effort, we looked at the effects of the Treatment Index on reproductive parameters. Results from generalized linear models indicated that treatment did not have an effect on vireo nesting effort or the number of vireo fledglings per pair produced in 2022. Similarly, we did not detect an effect of Treatment Index on daily survival rate (DSR) of nests. Analysis of vegetation data collected at vireo nests from 2006 to 2022 did not reveal an effect of vegetation cover at the nest on DSR. We did find, however, that Channel nests were placed higher in the host plant than Off-channel nests. In the Channel and Off-channel sites, successful nests were placed closer to the edge of the host plants than unsuccessful nests. Additionally, successful Off-channel nests were placed lower in the vegetation, in shorter host plants, and closer to the edge of the vegetation clump than unsuccessful nests. Red/arroyo willow ( Salix laevigata or Salix lasiolepis ) were the species most commonly selected for nesting by vireos in all three site types. Black willow ( Salix gooddingii ) and mule fat ( Baccharis salicifolia ) also were commonly used. Vireos used a wider variety of species for nesting in Channel and Off-channel sites (eight and six species, respectively) compared to Restoration sites (two species), although there was limited nesting in Restoration sites in 2022. There were 43 vireos banded before the 2022 breeding season that were resighted and identified at the Project Area in 2022, all of which were originally banded in the Project Area. Adult birds of known age ranged from 1 to 7 years old. A total of 146 vireos were newly banded in 2022. There were 8 adult vireos banded with a unique color combination, and 138 nestlings were banded with a single dark blue numbered federal band on the left leg. Between 2006 and 2022, survivorship of males (66±11 percent) was consistently higher than that of females (59±12 percent). First-year birds from 2006 to 2022 had an average annual survivorship of 15±6 percent. First-year dispersal in 2022 averaged 6.7±7.4 kilometers (km), with the longest dispersal (15.3 km) by a male that was recaptured at Fallbrook Creek, Fallbrook Naval Weapons Station (FNWS). From 2007 to 2011, most returning first-year vireos returned to the Project Area, whereas from 2014 to 2016, the majority of returning birds dispersed to areas outside of the Project Area. From 2018 to 2021, the trend shifted, and more first-year vireos returned to the Project area. In 2022, only one first-year vireo returned to the project area and two dispersed to sites outside the Project Area (upstream to the middle San Luis Rey River and to Fallbrook Creek, FNWS). However, the total number of identified first-year vireos was low and the trend in 2022 will likely shift as additional returning first-year vireos are identified in subsequent years. Most of the returning adult male vireos showed strong between-year site fidelity to their previous territories. Seventy-three percent of males (27/37) occupied a territory in 2022 that they had defended in 2021 (within 100 meters [m]). There were no females (0/4) detected in 2022 that returned to a territory they occupied in 2021; however, 50 percent of females (2/4) detected in 2022 returned to areas adjacent to their previous territories (within 300 m). The average between-year movement for returning adult vireos was 0.3±0.7 km. The amount of treatment at adults’ 2021 territories did not affect the distance adults moved to their 2022 territories. We completed four protocol surveys for the endangered Southwestern Willow Flycatcher ( Empidonax traillii extimus ; flycatcher) at the Project Area between May 16 and July 25, 2022. Four transient Willow Flycatchers were detected in the Project Area in 2022. Two transients were detected in Reach 1, one in Reach 3a, and one in Pilgrim Pond. There were not any resident flycatchers documented in the Project Area in 2022. A total of 46 vegetation transects (528 points) were sampled at the Project Area in 2022. Seventy-one percent (378/528) of points were located in the Channel, and 22 percent (115/528) were in Upper Pond. The remaining 7 percent (35/528) of points were at the Whelan Restoration site. Foliage cover below 2 m was higher at the Channel points compared to Upper Pond and Whelan Restoration, which can be attributed to the dense herbaceous vegetation that grows after mowing. Above 2 m, foliage cover was similar at the Channel and Whelan Restoration sites and was higher than at Upper Pond. Average canopy height was higher in the Channel (5.6±3.4 m) compared to Upper Pond (4.7±2.9 m) and Whelan Restoration (4.6±1.9 m). From 2006 to 2022, total foliage cover declined above 2 m in the Channel, in contrast to Upper Pond and Whelan Restoration, where little directional change in vegetation cover has occurred and where vegetation cover has largely recovered to 2006 levels. Within the Channel, the steepest declines occurred between 2009 and 2013 and between 2014 and 2016. Since 2016, we observed an increase in foliage cover, largely herbaceous, between 0 and 2 m within the Channel. The percent cover remained below levels detected before 2009 for other height classes. We sampled vegetation at 44 vireo nests and 44 random plots (“territory” plots) within territories in the Channel and Upper Pond after the 2022 breeding season. Vireos in the Channel established territories in areas with significantly more cover from 3 to 6 m but less cover below 2 m relative to the available habitat. Within territories, Channel vireos selected nest sites with significantly more foliage cover from 2 to 3 m. Vireos at Upper Pond established territories in areas with significantly more foliage cover from 5 to 6 m and below 1 m relative to available habitat. However, within territories, Upper Pond vireos selected nest sites with significantly less foliage cover from 5 to 6 m and below 1 m. Data either are not available or have limited availability owing to restrictions of the funding entity (U.S. Army Corps of Engineers). Please contact Christopher Chabot, Planning Division, Los Angeles District, U.S. Army Corps of Engineers, for more information.

Califoria↗

USGS2013

Method to support Total Maximum Daily Load development using hydrologic alteration as a surrogate to address aquatic life impairment in New Jersey streams

More than 300 ambient monitoring sites in New Jersey have been identified by the New Jersey Department of Environmental Protection (NJDEP) in its integrated water-quality monitoring and assessment report (that is, the 305(b) Report on general water quality and 303(d) List of waters that do not support their designated uses) as being impaired with respect to aquatic life; however, no unambiguous stressors (for example, nutrients or bacteria) have been identified. Because of the indeterminate nature of the broad range of possible impairments, surrogate measures that more holistically encapsulate the full suite of potential environmental stressors need to be developed. Streamflow alteration resulting from anthropogenic changes in the landscape is one such surrogate. For example, increases in impervious surface cover (ISC) commonly cause increases in surface runoff, which can result in “flashy” hydrology and other changes in the stream corridor that are associated with streamflow alteration. The NJDEP has indicated that methodologies to support a hydrologically based Total Maximum Daily Load (hydro-TMDL) need to be developed in order to identify hydrologic targets that represent a minimal percent deviation from a baseline condition (“minimally altered”) as a surrogate measure to meet criteria in support of designated uses. The primary objective of this study was to develop an applicable hydro-TMDL approach to address aquatic-life impairments associated with hydrologic alteration for New Jersey streams. The U.S. Geological Survey, in cooperation with the NJDEP, identified 51 non- to moderately impaired gaged streamflow sites in the Raritan River Basin for evaluation. Quantile regression (QR) analysis was used to compare flow and precipitation records and identify baseline hydrographs at 37 of these sites. At sites without an appropriately long period of record (POR) or where a baseline hydrograph could not be identified with QR, a rainfall-runoff model was used to develop simulated baseline hydrographs. The hydro-TMDL approach provided an opportunity to evaluate proportional differences in flow attributes between observed and baseline hydrographs and to develop complementary flow-ecology response relations at a subset of Raritan River Basin sites where available flow and ecological information overlapped. The New Jersey Stream Classification Tool (NJSCT) was used to determine the stream class of all 51 study sites by using either an observed or a simulated baseline hydrograph. Two New Jersey stream classes (A and C) were evaluated to help characterize the unique hydrology of the Raritan River Basin. In general, class C streams (1.99–40.7 square miles) had smaller drainage areas than class A streams (0.7–785 square miles). Many of the non-impaired and moderately impaired class A and C streams in the Raritan River Basin were found to have significant hydrologic alteration as indicated by numerous flow values that fell outside the established 25th-to-75th- and the more conservative 40th-to-60th-percentile boundaries. However, percent deviations for the class C streams (defined as moderately stable streams with moderately high base-flow contributions) were, in general, much larger than those for the class A streams (defined as semiflashy streams characterized by moderately low base flow). The greater deviations for class C streams in the hydro-TMDL assessments likely resulted from comparisons that were based solely on simulated baseline hydrographs, which were developed without considering any anthropogenic influences in the basin. In contrast, comparisons for many of the class A streams were made by using an observed baseline, which already includes an implicit level of ISC and other human influences on the landscape. By using the hydro-TMDL approach, numerous flow deviations were identified that were indicative of streams that are highly regulated by reservoirs or dams, streams that are affected by increasing amounts of surface runoff resulting from ISC, and streams that are affected by water abstraction (that is, groundwater or surface-water withdrawals used for agricultural and human supply). Eight of the reservoir- and (or) dam-affected sites showed flow deviations that are indicative of flow-managed systems. For example, indices that account for the timing and magnitude of high and low flows were often found to fall outside the 25th-to-75th-percentile range. In general, at regulated class C streams, annual summer low flows are arriving later and tend to be lower, and high flows are arriving earlier with higher magnitudes of longer duration. At class A streams, high and low flows are arriving later with an overall increase in discharge with respect to the prereservoir baseline conditions. The drainage basins of eight of the study sites had large values of ISC (>10 percent), most likely as a result of expanding urban development. In general, the magnitude and frequency of high flows at class A and C sites with high ISC are increasing and were commonly found to fall outside the 25th-to-75th-percentile range. Additionally, magnitudes of low flows are becoming lower and, although the timing of high flows was highly variable, low-flow events appeared to be arriving earlier than would be expected under normal low-flow conditions. Three of the study sites appeared to be affected by hydrologic changes associated with water abstraction. At these sites, the timing of flows appeared to be altered. For example, low flows tended to arrive earlier and high flows arrived later at two of the three sites. Additionally, the magnitude and duration of low flows were commonly less than the 25th-percentile value and the duration of high flows appeared to increase. A reduced set of hydrologic and ecological variables was used to develop univariate and multivariate flow-ecology response models for the aquatic-invertebrate assemblage. Many hydrologic variables accounting for the duration, magnitude, frequency, and timing of flows were significantly correlated with ecological response. Multiple linear regression (MLR) models were developed to provide a more holistic evaluation of the combined effects of hydrologic alteration and to identify models with two or three hydrologic variables that account for a significant proportion of the variability in invertebrate-assemblage condition as represented by assemblage metric scores. MLR models, derived on the basis of hydrologic attributes, accounted for 35 to 75 percent of the variability in assemblage condition. The hydro-TMDL method developed herein for non- to moderately impaired Raritan River Basin streams utilizes a “surrogate” approach in place of the traditional “pollutant of concern” approach commonly used for TMDL development. Managers can use the results obtained by using the hydro-TMDL method to offset the effects of impervious-surface runoff and altered streamflow and to implement measures designed to achieve the necessary load reductions for the “pollutant of concern” (that is, percentage deviations of stream-class-specific flow-index values outside the established 25th-to-75th-percentile range). In this case, such deviations could represent all or a subset of the altered flow indices that prevent the stream from meeting designated aquatic-life criteria. This hydro-TMDL uses a reference, or attainment stream approach for developing the TMDL endpoint. That is, either observed or simulated baseline hydrographs were selected as appropriate reference conditions on the basis of results of QR analysis and watershed modeling procedures, respectively. For any stream in the Raritan River Basin evaluated as part of this study, the hydro-TMDL can be expressed as the greatest amount of deviation in flow a stream can exhibit without violating the stream’s designated aquatic-life criteria. Use of this surrogate approach is appropriate because flows that fall outside the established percentile ranges are ultimately a function of many anthropogenic modifications of the landscape, including the amount of stormwater runoff generated from impervious surfaces within a given basin, the presence of manmade structures designed to retain or divert water, the magnitude of ground- and surface-water abstraction, and the presence of water-supply processes implemented to support human needs. In addition, the stream-type-specific flow indices used as the basis for the hydro-TMDL approach are useful for representing the hydrologic conditions of class A and C streams/basins because they incorporate the full spectrum of flow conditions (very low to very high) that occur in the stream system over a long period of time, as well as those flow properties that change as a result of seasonal variation. Ultimately, an estimate of the maximum percentage flow reduction that could be allowed will be needed to address the aquatic-life impairments in many of the study streams in the Raritan River Basin and will be necessary for identifying appropriate target flow conditions for hydro-TMDL implementation. As described in this report, a target flow value equal to the 25th- or 75th-percentile flow rate could be selected as the point useful for setting specific hydrologic targets. This selection, however, is a management decision that could vary depending on the designated use of the stream or other regulatory factors (for example, water-supply protection, trout production, antidegradation policies, or special protection designations). In New Jersey streams where no unambiguous stressors can be identified, State monitoring agencies, such as the NJDEP, could choose to require the implementation of a flow-based TMDL that not only supports designated uses, but meets the regulatory requirements under the Clean Water Act, and represents a balance between water supply intended to meet human needs and the conservation of ecosystem integrity.

New Jersey↗