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At least 1,063 records · Page 59Linked to original sources
USGS2018

Water temperature in the Lower Quinault River, Olympic Peninsula, Washington, June 2016 - August 2017

The availability of cold-water refugia during summertime river-water temperature maximums is important for cold-water fish species including Endangered Species Act listed salmonids since water temperature influences metabolism, growth, and phenology. The U.S. Geological Survey monitored water temperature at 10 sites approximately evenly-spaced along the lower Quinault River on the Olympic Peninsula, Washington, from June 2016 to August 2017 to assess thermal conditions in the lower river. During this 15-month period, there was a near-continuous, 15-minute record at 7 of the sites; complications with thermistors at 3 of the 10 sites limited the temperature dataset to include only summer 2016. In addition, near-streambed and water-surface temperatures were measured along the lower river during a longitudinal survey from August 9 to 12, 2016, during summer baseflow conditions to potentially identify cold or cooler water regions. Measured August water temperatures were warmer than model-predicted August temperatures for the period, 1993–2011. Summertime (July–September) daily minimum temperatures exceeded established salmon habitat threshold temperatures of 16 °C (core summer season) and 17.5 °C (spawning, rearing, and migration periods) for 122 and 65 days, respectively, on average at all monitoring sites with a complete 15-month record that included two summer baseflow periods. Summertime water temperatures at those sites were generally cooler in the downstream direction along the lower Quinault River but became warmer in the downstream direction during the rest of the year, suggesting the river was influenced by diffuse discharge of groundwater with a relatively constant annual temperature. The August longitudinal temperature survey did not detect cold-water refugia (features more than 3 °C cooler than ambient stream water), although it did identify 11 cooler water features (CWF) approximately 100–800 m in length that were 0.1 °C cooler than adjacent upstream or downstream water. The CWFs appeared to correspond to local geomorphic conditions. In August 2017, 10 of the 11 CWFs were field surveyed, and 5 appeared to be influenced by shading from solar radiation by riparian vegetation or steep cliff banks. In addition, field observations suggest that finer scale (that is, less than 10 m) CWFs, specifically individual side pools associated with large, in-channel wood, increased in frequency in the downstream direction along the lower Quinault River. However, this study did not quantify the density or water temperatures associated with these fine-scale features that may serve as cool- or cold-water pockets or patches.

Washington↗
USGS2018

Social attraction used to establish Caspian tern (Hydroprogne caspia) nesting colonies on modified islands at the Don Edwards San Francisco Bay National Wildlife Refuge, California—Final report

To address the 2008/2010 and Supplemental 2014 National Oceanic and Atmospheric Administration Fisheries Biological Opinion for operation of the Federal Columbia River Power System, the U.S. Army Corps of Engineers (USACE) and the Bureau of Reclamation (Reclamation) developed and began implementation of Caspian tern ( Hydroprogne caspia ) management plans. This implementation includes redistribution of the Caspian terns in the Columbia River estuary and the mid-Columbia River region to reduce predation on salmonids listed under the Endangered Species Act. Key elements of the plans are (1) reduction of nesting habitat for Caspian terns in the Columbia River estuary and the mid-Columbia River region, and (2) creation or modification of nesting habitat at alternative sites within the Caspian tern breeding range. As part of this effort, USACE and Reclamation developed Caspian tern nesting habitat at the U.S. Fish and Wildlife Service Don Edwards San Francisco Bay National Wildlife Refuge (DENWR), California, prior to the 2015 nesting season. Furthermore, nesting habitat for western snowy plovers ( Charadrius alexandrinus nivosus ) also was developed to provide separate nesting opportunities in the same managed ponds to reduce potential conflicts with Caspian terns. Specifically, seven recently constructed islands within two managed ponds (Ponds A16 and SF2) of DENWR were modified to provide habitat attractive to nesting Caspian terns (5 islands) and snowy plovers (2 islands). These 7 islands were a subset of 46 islands recently constructed in Ponds A16 and SF2 to provide waterbird nesting habitat as part of the South Bay Salt Pond (SBSP) Restoration Project. We used social attraction methods (decoys and electronic call systems) to attract Caspian terns and snowy plovers to these seven modified islands, and conducted surveys from March to September of 2015, 2016, and 2017 to evaluate nest numbers, nest density, and productivity. Results from the 2015 nesting season, the first year of the study, indicated that island modifications and social attraction measures were successful in establishing Caspian tern breeding colonies at Ponds A16 and SF2 of DENWR. Prior to 2015, there was no history of Caspian terns nesting in either Pond A16 or Pond SF2. The success of 2015 continued in 2016 and 2017. In 2017, the third and final year of the project, Caspian terns initiated at least 664 nests, fledged at least 239 chicks, and had a breeding success rate of 0.36 fledged chicks per breeding pair. This represents a 171 percent increase in the number of breeding pairs and a 41 percent increase in the number of chicks fledged, but a 48 percent decrease in the fledglings produced per breeding pair in 2017 compared to 2015, the first year the colonies were established. The two new large and growing Caspian tern nesting colonies at Ponds A16 and SF2 demonstrate the effectiveness of social attraction measures in helping to establish tern nesting colonies in San Francisco Bay. Social attraction measures similar to those used in this study, but targeting other colonial species such as Forster’s terns ( Sterna forsteri ) and American avocets ( Recurvirostra americana ), may help to establish waterbird breeding colonies at wetlands enhanced as part of the SBSP Restoration Project.

California↗
USGS2018

Effects of transmitter type, tagging method, body size, and temperature on behavior, physiology, and swimming performance of juvenile Chinook salmon (Oncorhynchus tshawytscha)

The objective of this study was to assess the impact of different tagging methods and transmitter types on juvenile salmonid behavior, mortality, physiology, and swimming performance over a range of water temperatures and fish sizes. In Chapter 1, two laboratory experiments were conducted to assess maximum burst-swimming speeds, the probability of gulping air, swimming angles, and the probability of resting on a screen in a swim tunnel. For the burst swim speed experiment, we identified a slightly reduced, but statistically significant difference in burst-swimming speeds for gastric- and surgical-tagged fish implanted with dummy radio and acoustic transmitters. For the swim tunnel experiment, surgical-tagged fish were one-half as likely to gulp air at the surface of the swim tunnel as untagged and gastric-tagged fish. We observed higher probabilities of fish gulping air at the surface for fish with tag ratios greater than 5 percent, suggesting that smaller fish required greater adjustment to their buoyancy than larger fish. We also observed that gastric-tagged fish had, on average, steeper swimming angles than untagged and surgical-tagged fish in the swim tunnel. In Chapter 2, we conducted a field-based laboratory experiment at John Day Dam to assess the sustained swimming performance (i.e., critical swimming speed or U crit ) of in-river migrating subyearling Chinook salmon that were surgically implanted with dummy radio and acoustic transmitters. Statistical tests indicated a significant reduction (about 8.3 centimeters per second [cm/s] or 1 body length per second) in sustained swimming performance for fish implanted with either radio or acoustic transmitters. We also found a significant reduction in U crit of -1.38 cm/s for every 1 degree Celsius (°C) increase in temperature. In Chapter 3, we assessed the effects of water temperature on the physiology, mortality, and swimming performance of juvenile Chinook salmon in laboratory and field experiments. Juvenile Chinook salmon generally showed elevated stress response, elevated mortality, and reduced swimming performance as water temperature increased. We concluded that the water temperature threshold for handling and tagging fish with minimal impacts seems to be near 23 °C. At 25 °C, we documented very high mortality and dramatically reduced swimming performance of tagged fish relative to controls. Telemetry studies conducted at 25 °C would not meet the critical assumption that the transmitter has minimal impacts on the study fish. In the Chapter 4, we evaluated the effects of antenna length and antenna material on the subsequent tag output power, reception, and detection of tagged fish. In a laboratory, we compared the relative signal strengths in water of 150-megahertz transmitters over a range of antenna lengths (from 6 to 30 cm) and materials (one weighing about one-half of the other). The peak relative signal strengths were at 20 and 22 cm, which are about 1 wavelength underwater at the test frequency. The peak relative signal strengths at these antenna lengths were about 50 percent greater than those of 30-cm antennas, a length commonly used in fisheries research.

Open-File Report↗
USGS2019

Effectiveness of fish screens in protecting lamprey (Entosphenus and Lampetra spp.) ammocoetes—Pilot testing of variable screen angle

Thousands of screened water diversions throughout the Columbia River Basin of the Pacific Northwest are sources of entrainment (unintended diversion into an unsafe passage route), injury, and mortality for a range of fish species and screening criteria have been developed to reduce and mitigate these effects. Large knowledge gaps exist concerning the potential effects of these screens on juvenile and larval lampreys ( Entosphenus and Lampetra spp. ) that may be particularly vulnerable to screening effects owing to their small size, unique morphology, and poor swimming performance. The few studies that have evaluated screen impacts for lampreys have compared common screen materials in a laboratory setting using a large, recirculating flume, and have reported that screen size and material influence the risk of entrainment. We compared entrainment rate, impingement rate and duration, injury rate, and delayed (24-hour) mortality of larval lamprey (ammocoetes) exposed to two screen angles. A 20-degree screen was tested because it is a common configuration, and a 12-degree screen was selected to represent a screen more parallel to flow than the 20-degree screen. We included juvenile rainbow trout ( Oncorhynchus mykiss ) in tests for both screen angles so that any screen interaction improvements observed for lamprey could be considered in light of their effect on salmonids ( Oncorhynchus spp. ). Study fish were released singly into the flume at two locations: near-screen (SCR) releases at about 30 centimeters upstream of the screen and mid-channel (MID) releases at about 1.4 meters upstream of the screen. We completed 120 screen trials with ammocoetes and 117 screen trials with juvenile tout during April–May 2018. Ammocoetes had short mean trial durations (less than 30 seconds) and were most frequently bypassed. Over one-half of the ammocoetes briefly (for less than 1 second) contacted the screen. Rates of screen contact were similar between the two screen angles, but higher for SCR releases (about 83–90 percent) than for MID releases (about 28–44 percent). Screen impingements were not common (8.3 percent of ammocoetes) and did not result in significant injury or delayed mortality. The final logistic regression model showed that screen angle and release location did not significantly affect whether ammocoetes were bypassed. The size of the lamprey, expressed as mass or length, was the only significant predictor of fate. We noted an estimated 4.7-percent increase in the odds of being bypassed for every 1-milligram increase in ammocoete mass and a 49-percent increase in the odds of being bypassed for every 1-millimeter increase in length. Trout did not experience negative effects with the 12-degree screen; they had short mean trial durations (less than 40 seconds) and limited contact with the screens (11.1 percent of trout), were most commonly bypassed, and none were entrained. Screen angle and release location were not significant drivers of fate for trout. The 12-degree and 20-degree screens performed comparably for both lamprey and trout and effectively bypassed these fishes. Some metrics showed advantages for the 12-degree screen, suggesting that screens installed more parallel to flow might warrant further testing.

Columbia River Basin↗
USGS2020

Fish and habitat assessment in Rock Creek, Klickitat County, southeastern Washington, 2018

Executive Summary Native steelhead (anadromous form of rainbow trout [ Oncorhynchus mykiss ]) and bridgelip sucker ( Catostomus columbianus ) were historically used by the Kah-miltpah (Rock Creek) Band for sustenance, trade, and traditional practices in Rock Creek, a tributary to the Columbia River in southeastern Washington State. Rock Creek flows south to the Columbia River at river kilometer (rkm) 368 and is an intermittent stream of great significance to the Yakama Nation and to the Kah-miltpah Band in particular. Concern over declines in the abundance of these fish in Rock Creek prompted a research and monitoring program to better understand habitat conditions, population status, and limiting factors. In addition to steelhead and bridgelip sucker, coho salmon ( Oncorhynchus kisutch ) and resident rainbow trout are also present and monitored. Rainbow trout and steelhead will be collectively referred to as O. mykiss . Streamflow is a limiting habitat factor in this system, but steelhead and coho salmon still successfully return to spawn, rear, outmigrate, and survive over summer in many of the isolated pools that provide important refuge for juvenile rearing. We completed a habitat survey during autumn 2018 to assess the perennial pools during low-flow conditions. In Rock Creek, the overall percentage of habitat recorded as dry was 41, non-pool wet was 42, and pool was 17. The number of pools ( n =93) recorded was less than during previous years’ survey efforts (2015–17). The percentage of non-pool wet habitat was generally higher in 2018 than in previous years. This is a likely result of habitat reaches, which in the past, were considered pools but have become shallower and smaller and are now categorized as non-pool wet habitat. However, the fewer habitat reaches categorized as pools in 2018 now have an average length, area, and depth that are generally greater than in past years. In Walaluuks Creek, the percentage of habitat recorded as dry was 53, non-pool wet was 40, and pool was 7. The percentage of pool habitat was the lowest of all years surveyed since 2015. Fish sampling occurred during autumn after habitat surveys were completed from October 1 to November 9. Fish species distribution, relative abundance, length-frequency distribution, and pool fish density were determined using backpack electrofishing in stratified, systematically selected pools. During fish sampling, 855 O. mykiss were handled and 662 were tagged with a passive integrated transponder (PIT) tag, and 718 coho salmon were handled and 567 were PIT tagged. A total of 536 bridgelip suckers and largescale suckers ( Catostomus macrocheilus [ n =6]) were handled and 294 were PIT tagged. In Rock Creek, pool abundance estimates were calculated for six pools for both O. mykiss age classes (age 0 and age 1 or older [age 1+]) and one additional pool for age 1+. For pools where age-0 O. mykiss were present, the average pool population abundance was 0.144 ( n =6; range: 0.052–0.208) fish per square meter. For age-1+ O. mykiss , the average pool population abundance was 0.045 ( n =7; range: 0.002–0.179) fish per square meter. For age-0 O. mykiss in Walaluuks Creek, the average pool abundance was 0.207 fish per square meter ( n =7; range: 0.038–0.416), and for age-1+ fish, the average pool abundance was 0.382 fish per square meter ( n =6; range: 0.009–0.761). In Rock Creek, coho salmon were more abundant than O. mykiss in pools except for three pools upstream from rkm 20. The average pool abundance for coho salmon was 0.256 fish per square meter ( n =8; range: 0.019–0.756) in Rock Creek pools. In Walaluuks Creek, coho salmon were captured in four pools and were not captured in the upstream pools sampled. The average pool abundance for coho salmon in the four lower pools was 0.488 fish per square meter ( n =4; range: 0.417–0.548). Bridgelip suckers were captured in all pools in Rock Creek except the pool sampled at rkm 21.8. The average pool abundance for bridgelip suckers was 0.552 fish per square meter ( n =7; range: 0.015–1.554) in Rock Creek. Bridgelip suckers were captured in three downstream pools in Walaluuks Creek, and the average abundance was 0.044 fish per square meter ( n =3; range: 0.024–0.085). Overwinter and reach survival probabilities were estimated for O. mykiss and coho salmon using a Cormack-Jolly-Seber modeling approach. The best fit survival model for the O. mykiss and coho salmon was a reach only model. The upstream reach includes overwinter survival probability because fish are tagged and released in autumn and primarily migrate the following spring. During 2018, coho salmon (0.568, standard error [SE]=0.027) had a significantly higher probability of overwinter survival than O. mykiss (0.276, SE=0.019). The reach survival probability was higher for O. mykiss than coho salmon in the downstream migratory reaches. Survival was not modeled for bridgelip suckers. For bridgelip suckers, 147 were detected of 294, that were PIT tagged and released in the Rock Creek subbasin (50.0 percent). Information provided in this report increases our understanding of the status and trends of these populations. It further documents how intermittent streams can support salmonid populations. It also provides insight into potential management and restoration actions that could be beneficial and timing and allocation of resources. Ongoing monitoring work of this population will inform progress towards Rock Creek species recovery goals and contribution to recovery goals for the steelhead Middle Columbia River Distinct Population Segment.

Washington↗
USGS2023

Simulating post-dam removal effects of hatchery operations and disease on juvenile Chinook salmon (Oncorhynchus tshawytscha) production in the Lower Klamath River, California

Executive Summary The Federal Energy Regulatory Commission has been considering the approval to breach four dams on lower Klamath River in southern Oregon and northern California. Approval of this application would allow for Strikeouts indicate text deletion hereafter. decommissioning and dam removal, beginning as early as 2023. This action would affect Klamath River salmon ( Oncorhynchus ssp.) populations, a critical food source for federally endangered Southern Resident Killer Whales ( Orcinus orca ). In the long run, reintroduction of salmon populations to the upper Klamath River Basin may increase salmon abundance available to Southern Resident Killer Whales, but in the near term, it is uncertain how changes in hatchery management and disease-caused mortality by the myxosporean parasite Ceratonova shasta will influence abundance of salmon populations entering the ocean. To assess this uncertainty, we used the Stream Salmonid Simulator (S3) to simulate population dynamics of juvenile Chinook salmon ( Oncorhynchus tshawytscha ) for nine different population sources that rear and migrate through the Klamath River. S3 is a spatially explicit population model that runs on a daily time-step and simulates daily growth, survival, and movement of juvenile Chinook salmon from the time of spawning through ocean entry. The key features of this model relevant to this report include (1) a C. shasta disease submodel; (2) a temperature-dependent bioenergetics model that calculates daily growth rates; (3) size-dependent movement; (4) density-dependent dynamics that are influenced by the effect of flow on suitable habitat area; and (5) habitat, river flow, and water temperature specific to each scenario. We constructed and ran four scenarios: two scenarios for dams in place (Dams In) and dams removed (Dams Out), and given these dam-removal conditions, a low- and high-spore scenario for C. shasta . Each scenario was run for nine water years representing a range of conditions from dry to wet. Previously published daily river flows and water temperatures for Dams In and Dams Out provided physical inputs for each scenario. Daily spore concentrations were simulated using a three-part mechanistic model that used river discharge, water temperature, and the prevalence of infection (POI) of hatchery-origin Chinook salmon juveniles with C. shasta in the previous year 3 . We constructed two spore scenarios for each Dams In and Dams Out scenario, a “Low Spore” scenario and a “High Spore” scenario resulting in four scenarios for comparison. Spore scenarios were established by setting the prior-year POI of hatchery fish to 0.15 and 0.75 in the estimation of spore concentrations. Hatchery releases under Dams Out differed from those under the current Dams In scenario. Hatchery releases under the Dams Out scenario were modified to emulate changes in hatchery production that would occur under Dams Out conditions. This included moving hatchery production and releases from Iron Gate Dam to a proposed hatchery at Fall Creek, which would be located about 11 kilometers (km) upstream of Iron Gate Dam. It is anticipated that the Fall Creek hatchery would produce fewer fish at smaller and larger sizes at different release timings. For salmon inputs, we used observed historical abundance of main-stem spawners from brood year 2009 and juvenile salmon entering from tributaries in water year 2010, which represented an average return year for the 2005–18 period. Main-stem spawning was allowed to shift upstream from Iron Gate Dam under the Dams Out scenario. We also included hatchery-origin fish as natural spawners that would have otherwise returned to Iron Gate Hatchery in the first 3 years following dam removal. The S3 model simulated considerably higher total abundance for Dams Out relative to the respective Dams In scenarios, and higher abundance for the Low Spore scenario relative to the High Spore scenario. The difference in abundance between the four combinations of the dam-removal and spore scenarios varied among population groups. For main-stem natural production, juvenile abundance at ocean entry was 2–3 times higher for Dams Out scenarios than for Dams In scenarios, and juvenile abundance for High Spore scenarios was lower than that for the Dams Out Low Spores scenario. For hatchery releases, abundance at ocean entry was similar between Dams In and Dams Out scenarios for most water years, despite lower release sizes from Fall Creek Hatchery under Dams Out. For tributary populations, abundance for the High Spore scenarios was consistently lower than for the Low Spore scenarios, but differences between dam-removal scenarios varied among water years, with Dams Out scenarios having similar or higher abundance than Dams In scenarios, and dry water years having the largest difference between Dams In and Dams Out scenarios. We determined that different factors affected the response of each population group. For main-stem natural production, survival from fry emergence to ocean entry was higher under Dams Out scenarios compared to Dams In scenarios because juveniles emerged later and tended to arrive at the ocean sooner and at larger sizes, causing the population to have less time-dependent in-river mortality. Owing to their late release timing, hatchery populations had high disease-caused mortality in Dams In and Dams Out High Spore scenarios. Furthermore, a high proportion of infected fish (those that would be expected to die at some future point) survived to the ocean. Iron Gate Hatchery fish had lower survival rates than releases from Fall Creek Hatchery because the last mid-June release group from the 2010 Iron Gate Hatchery release incurred nearly total mortality in most water years owing to water temperatures exceeding 24 degrees Celsius. Our analysis shows how the S3 model was able to track different populations and provide insights on how the differential response of each population combined to influence the simulated number of juvenile Chinook salmon arriving at the Pacific Ocean where they become available as a food source for Southern Resident Killer Whales.

California↗
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↗
USGS2024

A machine learning tool for design of behavioral fish barriers in the Sacramento-San Joaquin River Delta

Executive Summary Survival of out-migrating juvenile salmonids ( Oncorhynchus spp.) through the Sacramento-San Joaquin River Delta averages less than 33 percent, depending on water flow through the delta, and is partially governed by the distribution of fish among three Sacramento River distributaries: Sutter, Steamboat, and Georgiana sloughs. Behavioral altering structures in the junctions of the distributaries can effectively increase entrainment into favorable routes, thereby increasing through-delta (Verona to Chips Island, California) survival. The effectiveness of these structures, hence forth called “behavioral barriers,” are dependent on shape, length, location, barrier type, and water velocity, which is governed by Sacramento River discharge (hereinafter referred to as “flow”). We developed a machine learning tool to optimize behavioral barrier designs at up to three junctions within the Sacramento-San Joaquin Delta for improving through-delta survival of juvenile winter-run Chinook salmon ( Oncorhynchus tshawytscha ). This barrier optimization tool (BOT) works by evolving barrier solutions in one to three junctions by repeatedly simulating survival of populations of Sacramento River origin fish as they pass through the Delta. Over approximately 6,000 simulations per junction, the BOT converges on barrier designs that result in the greatest average survival given simulated environmental conditions. Survival at each iteration of the model is simulated using a modified version of the salmon travel time and routing simulation (STARS) model. In the BOT, STARS is modified by replacing probabilistic route determinations with an individual based model (IBM) that simulates fish behavior to predict the entrainment rates in each junction. The IBM allows the flexibility to explore how entrainment changes with evolving barrier designs. We used juvenile winter-run-sized Chinook salmon catch data collected at Knights Landing from 1997 to 2011 to create realistic arrival and spatial distributions of simulated fish within the BOT that varied among water years (hereafter years). We demonstrated the capabilities of the BOT by comparing optimized barrier solutions and their resulting simulated improvement in survival among three scenarios that differed in the number of junctions with barriers (Georgiana Slough, Steamboat Slough, or both) and the barrier operational period (early: November 1–March 15, or late: January 1–April 30). In this initial demonstration of the BOT we only considered a bioacoustic fish fence (BAFF) at Georgiana Slough and a floating fish guidance structure (FFGS) at Steamboat Slough. The increase in simulated through-delta fish survival ranged from 1.0 to 6.3 percent among the optimized barrier designs. The most effective Georgiana Slough barrier design predicted improved survival by 6.3 percent and was chosen by the California Department of Water Resources (DWR) as the Georgiana Slough salmon migratory barrier planned for operation annually from 2023 to 2030 at Georgiana Slough in response to the 2020 California Department of Fish and Wildlife’s (CDFW) Incidental Take Permit Minimization Measure 8.9.1 (California Department of Fish and Wildlife [CDFW], 2020). When barriers were simulated in both junctions, the percentages of simulated winter-run Chinook salmon interacting with a barrier at Steamboat or Georgiana sloughs were 95 percent given the early operational period and 48 percent given the late operational period. When barriers were simulated at both sloughs, the optimal barrier at Steamboat Slough effectively routed fish into the Sacramento River. This is because the Georgiana Slough barrier reduced routing into Georgiana Slough where survival is low, which resulted in higher survival for fish routed down the Sacramento River at Steamboat Slough than fish routed down Steamboat Slough. Whereas when no barrier was simulated at Georgiana Slough, the optimized barrier at Steamboat Slough routed fish into Steamboat Slough. This is because survival was higher through Steamboat Slough than the Sacramento River and Georgiana Slough combined. The greatest improvement in survival (6.3 percent) was predicted over the earlier operational period with only a barrier at Georgiana Slough.

California↗
USGS2025

Review of the Lake Washington Ship Canal and Ballard Locks model, Seattle, Washington, 2014–20

Executive Summary The Hiram M. Chittenden (Ballard) Locks and Lake Washington Ship Canal connect freshwater Lake Washington and saline Shilshole Bay of Puget Sound in Seattle, Washington. The locks and canal allow for ships to traverse this reach. Anadromous salmonids also migrate through, transitioning between saline and freshwater environments, and making use of a fish ladder at the locks when traveling upstream. WEST Consultants, Inc., constructed a two-dimensional hydrodynamic and water-quality model (CE-QUAL-W2) simulating flow, water temperature, and salinity for the Ballard Locks and the Lake Washington Ship Canal. An initial model was built for calendar years 2014–15, and the model was updated using a more recent and modern dataset for calendar years 2016–20. The U.S. Army Corps of Engineers requested that the U.S. Geological Survey review this model and its documentation to evaluate the technical aspects of its development and calibration. Findings from this review include the following: Overall, the Lake Washington Ship Canal CE-QUAL-W2 model was well-documented and constructed largely following typical model-development methods. The Lake Washington Ship Canal model was built with CE-QUAL-W2 model version 4.5, compiled and released by Portland State University in April 2021. CE-QUAL-W2 updates and improvements are regularly released with bug fixes and new features, so any model updates would benefit from the use of the most-recent software release. The model grid that represents the Lake Washington Ship Canal bathymetry was 9.2 kilometers (5.7 miles) long, matching the expected length of the waterway. The deepest model segments were near sampling site LLLW (Large Locks site) near the locks. Lake Union is reported to constitute most of the volume of the Lake Washington Ship Canal and is depicted as such in the model grid. The model includes several water outflows at Ballard Locks, including the large and small locks, a saltwater drain, a spillway, smolt flumes, and a fish ladder. Flows from the spillway, smolt flumes, and fish ladder were combined into one structure outflow in the model and assigned one withdrawal elevation from the Lake Washington Ship Canal. The smolt flume and spillway withdraw from the same elevation, but the fish ladder flow withdraws from a higher elevation in Lake Washington Ship Canal, and that flow could be separated into its own withdrawal. The model input files were created using the Coordinated Universal Time standard instead of the more typical choice of using local standard time. This is not incorrect, but sub-daily results would need to be converted to local time for science-communication purposes. The meteorological dataset had some unexpected anomalies, such as a baseline shift in the wind-speed dataset. Other nearby meteorological datasets could be used instead or used to correct the current meteorological inputs. The upstream boundary was configured with water-temperature data from a continuous monitor buoy in Lake Washington. The boundary salinity was set at 0 parts per thousand for the duration of the model simulation. A more realistic estimate of salinity at the upstream boundary could be constructed using data from the same buoy. Saline inflow at the downstream boundary of the Lake Washington Ship Canal model through lock exchanges at the large lock was included as a tributary in the model. Salinity and temperature inputs in this tributary at the large locks were set as constant values for the entire simulation. Saline inflow through the small lock was not included in the model because few data were available, and the input was likely to be small because of the smaller surface area and volume of the small lock relative to the large lock. The model did not include any flow, water temperature, or salinity inputs to the Lake Washington Ship Canal other than at the locks and at the upstream boundary. Any point sources, small tributaries, or stormwater inputs were omitted from the model. It is unclear whether this is a substantial omission relative to model results. Most model parameters were set as defaults or to reasonable values. However, the value of the WINDH parameter, the height of the wind speed measurement, was different than the height of the meteorological site. Compared to measured data, the model simulated water-surface elevations and water temperatures with reasonable accuracy. Differences in the modeled and measured salinities revealed some opportunities to improve the simulation of salinity, both baseline salinity and the salinity maxima in summer and autumn.

Washington↗
USGS2025

Rapid structured decision making for Hypomesus transpacificus (delta smelt) summer–fall freshwater outflow management

Managers of the Central Valley Project (CVP) and State Water Projects (SWP) in California are confronted with difficult tradeoffs between water uses and associated values affected by water management decisions. These decisions involve altering the timing and magnitude of water releases from dams and reservoirs, which can affect habitats for economically important and Federally and State-listed endangered fish species, water deliveries for agriculture or municipalities, and water quality. In this report, we describe the results of a rapid structured decision-making process used to assist management agencies in evaluating tradeoffs while gathering input from cooperating agencies, rightsholders, or interested parties (hereafter participants) through facilitated workshops in spring 2025. Consideration of alternative water management actions was initiated by the continued decline of Hypomesus transpacificus (delta smelt) populations and the issuance of a new biological opinion for the CVP and SWP long-term operations on the effects on delta smelt and other Endangered Species Act-listed species in November 2024. An Executive Order was also issued in January 2025, directing the Bureau of Reclamation to maximize water deliveries. Participants, led by the U.S. Geological Survey and cooperating agencies, identified 8 fundamental values (hereafter objectives) and 11 alternative water management scenarios (or “alternative management actions” based on the PrOACT model). Using multicriteria decision analysis, we evaluated performance (or “consequences” based on a consequence table analysis) and analyzed tradeoffs of alternative water management actions to the fundamental objectives. We ranked the alternative water management actions based on four participants’ objective weights and composite utility scores calculated using a linear value function. The three highest ranking alternative water management actions had the poorest performance for delta smelt but performed best for CVP and SWP water exports and objectives related to coldwater pool operations for salmonids. An optimum strategy that could prevent the extinction of delta smelt was not determined for this study. However, insights gained from our rapid decision analysis suggested nonflow scenarios could benefit the delta smelt population, including in drier years, and could be considered to avoid curtailment of water exports.

Open-File Report↗
USGS2004

Water-quality and biological conditions in the Lower Boise River, Ada and Canyon Counties, Idaho, 1994-2002

The water quality and biotic integrity of the lower Boise River between Lucky Peak Dam and the river's mouth near Parma, Idaho, have been affected by agricultural land and water use, wastewater treatment facility discharge, urbanization, reservoir operations, and river channel alteration. The U.S. Geological Survey (USGS) and cooperators have studied water-quality and biological aspects of the lower Boise River in the past to address water-quality concerns and issues brought forth by the Clean Water Act of 1977. Past and present issues include preservation of beneficial uses of the river for fisheries, recreation, and irrigation; and maintenance of high-quality water for domestic and agricultural uses. Evaluation of the data collected from 1994 to 2002 by the USGS revealed increases in constituent concentrations in the lower Boise in a downstream direction. Median suspended sediment concentrations from Diversion Dam (downstream from Lucky Peak Dam) to Parma increased more than 11 times, nitrogen concentrations increased more than 8 times, phosphorus concentrations increased more than 7 times, and fecal coliform concentrations increased more than 400 times. Chlorophyll-a concentrations, used as an indicator of nutrient input and the potential for nuisance algal growth, also increased in a downstream direction; median concentrations were highest at the Middleton and Parma sites. There were no discernible temporal trends in nutrients, sediment, or bacteria concentrations over the 8-year study. The State of Idaho?s temperature standards to protect coldwater biota and salmonid spawning were exceeded most frequently at Middleton and Parma. Suspended sediment concentrations exceeded criteria proposed by Idaho Department of Environmental Quality most frequently at Parma and at all but three tributaries. Total nitrogen concentrations at Glenwood, Middleton, and Parma exceeded national background levels; median flow-adjusted total nitrogen concentrations at Middleton and Parma were higher than those in undeveloped basins sampled nationwide by the USGS. Total phosphorus concentrations at Glenwood, Middleton, and Parma also exceeded those in undeveloped basins. Macroinvertebrate and fish communities were used to evaluate the long-term integration of water-quality contaminants and loss of habitat in the lower Boise. Biological integrity of the macroinvertebrate population was assessed with the attributes (metrics) of Ephemeroptera, Plecoptera, and Trichoptera (EPT) richness and metrics used in the Idaho River Macroinvertebrate Index (RMI): taxa richness; EPT richness; percent dominant taxon; percent Elmidae (riffle beetles); and percent predators. Average EPT was about 10, and RMI scores were frequently below 16, which indicated intermediate or poor water quality. The number of EPT taxa and RMI scores for the lower Boise were half those for least-impacted streams in Idaho. The fine sediment bioassessment index (FSBI) was used to evaluate macroinvertebrate sediment tolerance. The FSBI scores were lower than those for a site upstream in the Boise River Basin near Twin Springs, a site not impacted by urbanization and agriculture, which indicated that the lower Boise macroinvertebrate population may be impacted by fine sediment. Macroinvertebrate functional feeding groups and percent tolerant species, mainly at Middleton and Parma, were typical of those in areas of degraded water quality and habitat. The biological integrity of the fish population was evaluated using the Idaho River Fish Index (RFI), which consists of the 10 metrics: number of coldwater native species, percent sculpin, percent coldwater species, percent sensitive native individuals, percent tolerant individuals, number of nonindigenous species, number of coldwater fish captured per minute of electrofishing, percent of fish with deformities (eroded fins, lesions, or tumors), number of trout age classes, and percent carp. RFI scores for lower Boise sites indicated a d

Scientific Investigations Report↗
USGS2004

Water-quality data from 2002 to 2003 and analysis of data gaps for development of total maximum daily loads in the Lower Klamath River Basin, California

The U.S. Geological Survey (USGS) collected water-quality data during 2002 and 2003 in the Lower Klamath River Basin, in northern California, to support studies of river conditions as they pertain to the viability of Chinook and Coho salmon and endangered suckers. To address the data needs of the North Coast Regional Water Quality Control Board for the development of Total Maximum Daily Loads (TMDLs), water temperature, dissolved oxygen, specific conductance, and pH were continuously monitored at sites on the Klamath, Trinity, Shasta, and Lost Rivers. Water-quality samples were collected and analyzed for selected nutrients, organic carbon, chlorophyll-a, pheophytin-a, and trace elements. Sediment oxygen demand was measured on the Shasta River. Results of analysis of the data collected were used to identify locations in the Lower Klamath River Basin and periods of time during 2002 and 2003 when river conditions were more likely to be detrimental to salmonid or sucker health because of occasional high water temperatures, low dissolved oxygen, and conditions that supported abundant populations of algae and aquatic plants. The results were also used to assess gaps in data by furthering the development of the conceptual model of water flow and quality in the Lower Klamath River Basin using available data and the current understanding of processes that affect water quality and by assessing needs for the develoment of mathematical models of the system. The most notable gap in information for the study area is in sufficient knowledge about the occurrence and productivity of algal communities. Other gaps in data include vertical water-quality profiles for the reservoirs in the study area, and in an adequate understanding of the chemical oxygen demands and the sediment oxygen demands in the rivers and of the influence of riparian shading on the rivers. Several mathematical models are discussed in this report for use in characterizing the river systems in the study area; also discussed are the specific data needed for the models, and the spatial and temporal data available as boundary conditions. The models will be useful for the future development of TMDLs for temperature, nutrients, and dissolved oxygen and for assessing the role of natural and anthropogenic sources of heat, oxygen-producing and -consuming substances, and nutrients in the Klamath, Shasta, and Lost Rivers.

Scientific Investigations Report↗
USGS2007

Influence of Cougar Reservoir Drawdown on Sediment and DDT Transport and Deposition in the McKenzie River Basin, Oregon, Water Years 2002-04

Construction of a selective withdrawal tower at Cougar Reservoir in the South Fork McKenzie River, Oregon, during 2002-05 resulted in a prolonged release of sediment and high-turbidity water to downstream reaches throughout the summer of 2002, with additional episodic releases during storms in the following winters. Suspended-sediment concentrations and loads at five continuously monitored turbidity and discharge gaging stations were estimated using regression methods. Deposition in salmonid spawning beds was measured using infiltration bags. Stations were located upstream and downstream of Cougar Reservoir in the South Fork McKenzie River, in the mainstem of the McKenzie River upstream of the South Fork and downstream of Blue River, and in Blue River downstream of Blue River Reservoir. During 2002, Cougar Reservoir released approximately 17,000 tons of suspended sediment into the South Fork McKenzie River, or more than twice the incoming load from the South Fork upstream of the reservoir. In 2003 and 2004, the release of sediment from Cougar Reservoir decreased to 10,900 and 4,100 tons, respectively. Although Cougar Reservoir likely was a substantial source of sediment to the lower reaches during water years 2002 and 2003, the lack of continuous turbidity monitoring at stations other than the South Fork McKenzie River prior to January 2003 prevents quantification of the actual contribution to the mainstem. During water year 2004, the only year with complete records at all sites, Cougar Reservoir released about 24 percent (4,100 tons) of the sediment load estimated on the mainstem near Vida (16,900 tons); however, the relative contribution of Cougar Reservoir is expected to have been substantially larger during 2002 and 2003 when the newly exposed river channel in the upper reaches of the reservoir was actively eroding and migrating. Deposition of fine (less than 0.063-millimeter diameter) sediment into spawning beds, measured with the use of deployed infiltration bags, was greatest downstream of Cougar and Blue River Reservoirs (1.0 and 1.2 percent of total sediments, respectively). Deposition was least in the high-energy, unregulated environments (about 0.25 percent) of the South Fork McKenzie River above Cougar Reservoir and in the mainstem above the South Fork, and intermediate near Vida, the most downstream site on the mainstem. DDT, applied throughout much of the upper McKenzie River drainage basin to control spruce budworm during the 1950s, was detected in the South Fork near Rainbow in the form of its metabolites DDD and DDE in fine sediment captured in the infiltration bags. DDE also was detected in infiltration bags deployed in the McKenzie River near Vida, downstream of the South Fork. All concentrations of DDD and DDE were less than the aquatic-life criterion for bed sediment. DDT species were not detected in water samples, including samples collected during large storms. The reservoir apparently acted as a trap for sediment and DDT throughout the course of its existence, facilitating degradation of the trapped DDT, and may have been a source for both during the construction period in 2002-05, but the lack of detections during storms indicates that DDT transport was small. Transport of detectable amounts of DDT likely was limited to periods of high suspended-sediment concentrations (greater than 75-100 milligrams per liter). Infiltration bags were deployed during August 2003-July 2004 and were a useful device for measuring fine-sediment deposition and for chemical analysis of the deposited material. Deposition of fine-grained sediment downstream of the flood-control dams may be reduced if bed-moving events can be periodically reintroduced to those reaches.

Scientific Investigations Report↗
USGS2008

Conceptual Model of Hydrologic and Thermal Conditions of the Eastbank Aquifer System near Rocky Reach Dam, Douglas County, Washington

The Lower and Combined Aquifers of the Eastbank Aquifer system, located in a river-terrace deposit along the Columbia River near Rocky Reach Dam, Washington, are primarily recharged by the Columbia River and provide water to the Eastbank Hatchery and the regional water system servicing the cities of Wenatchee, East Wenatchee, and parts of unincorporated Chelan and Douglas Counties. In 2006, mean annual pumpage from the aquifers by the hatchery and regional water system was about 43 and 16 cubic feet per second, respectively. Reportedly, temperatures of ground water pumped by the hatchery have been increasing, thereby making water potentially too warm for salmonid fish production. An evaluation of hourly ground-water and river temperatures from January 1991 through August 2007 indicates increasing interannual trends in temperatures in most of the Lower and Combined Aquifers from 1999 through 2006 that correspond to increasing trends in the annual mean and annual maximum river temperatures during the same period of 0.07 and 0.17?C per year, respectively. There were no trends in the annual minimum river temperatures from 1999 through 2006, and there were no trends in the annual minimum, mean, and maximum river temperatures from 1991 through 1998 and from 1991 through 2007. Increases in river temperatures from 1999 through 2006 are within the natural variability of the river temperatures. Most of the Lower and Combined Aquifers reached thermal equilibrium?defined by constant time lags between changes in river temperatures and subsequent changes in ground-water temperatures?during 1991?98. The only exceptions are the Combined Aquifer north of the well field of the regional water system, which had not reached thermal equilibrium by 2006, and the Lower Aquifer west of the well fields of the hatchery and the regional water system, which reached thermal equilibrium prior to 1991. Because most of the Lower and Combined Aquifers were in thermal equilibrium from 1999 through 2006 and seasonal pumpage patterns were relatively stable, reported trends of increasing temperatures of water pumped by the hatchery well field are most likely explained by increasing trends in river temperatures. Most of the water pumped by the hatchery well field recharges in an area west to southwest of the well field about 2 months prior to the time it is pumped from the aquifer. The northern extent of the hatchery well field may pump some colder water from a bedrock depression to the north and west of the well field. The conceptual model of hydrologic and thermal conditions is supported by analyses of historical water temperatures, water-level data collected on July 18, 2007, and dissolved-constituent and bacterial concentrations in samples collected on August 20?22, 2007.

Scientific Investigations Report↗
USGS2010

Water quality and hydrology of the Silver River Watershed, Baraga County, Michigan, 2005-08

The Silver River Watershed comprises about 69 square miles and drains part of northeastern Baraga County, Michigan. For generations, tribal members of the Keweenaw Bay Indian Community have hunted and fished in the watershed. Tribal government and members of Keweenaw Bay Indian Community are concerned about the effect of any development within the watershed, which is rural, isolated, and lightly populated. For decades, the area has been explored for various minerals. Since 2004, several mineral-exploration firms have been actively investigating areas within the watershed; property acquisition, road construction, and subsurface drilling have taken place close to tributary streams of the Silver River. The U.S. Geological Survey, in cooperation with Keweenaw Bay Indian Community, conducted a multi-year water-resources investigation of the Silver River Watershed during 2005-08. Methods of investigation included analyses of streamflow, water-quality sampling, and ecology at eight discrete sites located throughout the watershed. In addition, three continuous-record streamgages located within the watershed provided stage, discharge, specific conductance, and water-temperature data on an hourly basis. Water quality of the Silver River Watershed is typical of many streams in undeveloped areas of Upper Michigan. Concentrations of most analytes typically were low, although several exceeded applicable surface-water-quality standards. Seven samples had concentrations of copper that exceeded the Michigan Department of Environmental Quality standards for wildlife, and one sample had concentrations of cyanide that exceeded the same standards. Concentrations of total mercury at all eight sampling sites exceeded the Great Lakes Basin water-quality standard, but the ratio of methylmercury to total mercury was similar to the 5 to 10 percent found in most natural waters. Concentrations of arsenic and chromium in bed sediments were near the threshold-effect concentration. A qualitative ecological assessment of fishes and macroinvertebrates showed that intolerant salmonids were present at most sampled sites, and macroinvertebrate communities were indicative of near-excellent or excellent conditions at all eight sites. This baseline information will aid in an ongoing monitoring effort designed to protect the water resources of the

Scientific Investigations Report↗
USGS2010

Regional Regression Equations to Estimate Flow-Duration Statistics at Ungaged Stream Sites in Connecticut

Multiple linear regression equations for determining flow-duration statistics were developed to estimate select flow exceedances ranging from 25- to 99-percent for six 'bioperiods'-Salmonid Spawning (November), Overwinter (December-February), Habitat Forming (March-April), Clupeid Spawning (May), Resident Spawning (June), and Rearing and Growth (July-October)-in Connecticut. Regression equations also were developed to estimate the 25- and 99-percent flow exceedances without reference to a bioperiod. In total, 32 equations were developed. The predictive equations were based on regression analyses relating flow statistics from streamgages to GIS-determined basin and climatic characteristics for the drainage areas of those streamgages. Thirty-nine streamgages (and an additional 6 short-term streamgages and 28 partial-record sites for the non-bioperiod 99-percent exceedance) in Connecticut and adjacent areas of neighboring States were used in the regression analysis. Weighted least squares regression analysis was used to determine the predictive equations; weights were assigned based on record length. The basin characteristics-drainage area, percentage of area with coarse-grained stratified deposits, percentage of area with wetlands, mean monthly precipitation (November), mean seasonal precipitation (December, January, and February), and mean basin elevation-are used as explanatory variables in the equations. Standard errors of estimate of the 32 equations ranged from 10.7 to 156 percent with medians of 19.2 and 55.4 percent to predict the 25- and 99-percent exceedances, respectively. Regression equations to estimate high and median flows (25- to 75-percent exceedances) are better predictors (smaller variability of the residual values around the regression line) than the equations to estimate low flows (less than 75-percent exceedance). The Habitat Forming (March-April) bioperiod had the smallest standard errors of estimate, ranging from 10.7 to 20.9 percent. In contrast, the Rearing and Growth (July-October) bioperiod had the largest standard errors, ranging from 30.9 to 156 percent. The adjusted coefficient of determination of the equations ranged from 77.5 to 99.4 percent with medians of 98.5 and 90.6 percent to predict the 25- and 99-percent exceedances, respectively. Descriptive information on the streamgages used in the regression, measured basin and climatic characteristics, and estimated flow-duration statistics are provided in this report. Flow-duration statistics and the 32 regression equations for estimating flow-duration statistics in Connecticut are stored on the U.S. Geological Survey World Wide Web application ?StreamStats? (http://water.usgs.gov/osw/streamstats/index.html). The regression equations developed in this report can be used to produce unbiased estimates of select flow exceedances statewide.

Scientific Investigations Report↗
USGS2014

Water-quality and biological conditions in selected tributaries of the Lower Boise River, southwestern Idaho, water years 2009-12

Water-quality conditions were studied in selected tributaries of the lower Boise River during water years 2009–12, including Fivemile and Tenmile Creeks in 2009, Indian Creek in 2010, and Mason Creek in 2011 and 2012. Biological samples, including periphyton biomass and chlorophyll-a, benthic macroinvertebrates, and fish were collected in Mason Creek in October 2011. Synoptic water-quality sampling events were timed to coincide with the beginning and middle of the irrigation season as well as the non-irrigation season, and showed that land uses and irrigation practices affect water quality in the selected tributaries. Large increases in nutrient and sediment concentrations and loads occurred over relatively short stream reaches and affected nutrient and sediment concentrations downstream of those reaches. Escherichia coli (E. coli) values increased in study reaches adjacent to pastured lands or wastewater treatment plants, but increased E. coli values at upstream locations did not necessarily affect E. coli values at downstream locations. A spatial loading analysis identified source areas for nutrients, sediment, and E. coli , and might be useful in selecting locations for water-quality improvement projects. Effluent from wastewater treatment plants increased nutrient loads in specific reaches in Fivemile and Indian Creeks. Increased suspended-sediment loads were associated with increased discharge from irrigation returns in each of the studied tributaries. Samples collected during or shortly after storms showed that surface runoff, particularly during the winter, may be an important source of nutrients in tributary watersheds with substantial agricultural land use. Concentrations of total phosphorus, suspended sediment, and E. coli exceeded regulatory water-quality targets or trigger levels at one or more monitoring sites in each tributary studied, and exceedences occurred during irrigation season more often than during non-irrigation season. As with water-quality sampling results, bottom-sediment samples analyzed for contaminants of emerging concern indicated that adjacent land uses can affect in-stream conditions. Contaminants of emerging concern were detected in four categories: urban compounds, industrial compounds, fecal steroids, and personal care products. Compounds in one or more of the four contaminant categories were detected at higher concentrations in upstream sites than in downstream sites in the tributaries and in the lower Boise River. High concentrations of compounds in upstream locations indicated that adjacent land use might be an important factor in contributing contaminants of emerging concern to the lower Boise River watershed. Expanded monitoring at Mason Creek near the mouth included a streamgage, a continuous water-quality monitor, and monthly water-quality sample collection. Data collected during expanded monitoring efforts at Mason Creek near the mouth provided information to develop and compare water-quality models. Regression models were developed using turbidity, discharge, and seasonality as surrogates to estimate concentrations of water-quality constituents. Daily streamflow also was used in a load model to estimate daily loads of water-quality constituents. Surrogate regression models may be useful for long-term monitoring and generally performed better than other models to estimate concentrations and loads of total phosphorus, total nitrogen, and suspended sediment in Mason Creek. Biological sampling results from Mason Creek showed low periphyton biomass and chlorophyll-a concentrations compared to those historically measured in the Boise River near Parma, Idaho, during October and November. The most abundant invertebrate found in Mason Creek was the highly tolerant and invasive New Zealand mudsnail ( Potamopyrgus antipodarum ). The presence of small rainbow trout (90 millimeters) may indicate salmonid spawning in Mason Creek. The rangeland-fish-index score of 58 for Mason Creek is comparable to rangeland-fish-index scores calculated for the Boise River near Middleton, indicating intermediate biotic condition.

Idaho↗
USGS2014

Hydrogeologic framework and groundwater/surface-water interactions of the South Fork Nooksack River Basin, northwestern Washington

A hydrogeologic framework of the South Fork (SF) Nooksack River Basin in northwestern Washington was developed and hydrologic data were collected to characterize the groundwater-flow system and its interaction with surface‑water features. In addition to domestic, agricultural, and commercial uses of groundwater within the SF Nooksack River Basin, groundwater has the potential to provide ecological benefits by maintaining late-summer streamflows and buffering stream temperatures. Cold-water refugia, created and maintained in part by groundwater, have been identified by water-resource managers as key elements to restore the health and viability of threatened salmonids in the SF Nooksack River. The SF Nooksack River drains a 183-square mile area of the North Cascades and the Puget Lowland underlain by unconsolidated glacial and alluvial sediments deposited over older sedimentary, metamorphic, and igneous bedrock. The primary aquifer that interacts with the SF Nooksack River was mapped within unconsolidated glacial outwash and alluvial sediment. The lower extent of this unit is bounded by bedrock and fine-grained, poorly sorted unconsolidated glaciomarine and glaciolacustrine sediments. In places, these deposits overlie and confine an aquifer within older glacial sediments. The extent and thickness of the hydrogeologic units were assembled from mapped geologic units and lithostratigraphic logs of field-inventoried wells. Generalized groundwater-flow directions within the surficial aquifer were interpreted from groundwater levels measured in August 2012; and groundwater seepage gains and losses to the SF Nooksack River were calculated from synoptic streamflow measurements made in the SF Nooksack River and its tributaries in September 2012. A subset of the field-inventoried wells was measured at a monthly interval to determine seasonal fluctuations in groundwater levels during water year 2013. Taken together, these data provide the foundation for a future groundwater-flow model of the SF Nooksack River Basin that may be used to investigate the potential effects of future climate change, land use, and groundwater pumping on water resources in the study area. Site-specific hydrologic data, including time series of longitudinal temperature profiles measured with a fiber-optic distributed temperature sensor and continuous monitoring of stream stage and water levels measured in wells in adjacent wetlands and aquifers, also were measured to characterize the interaction among the SF Nooksack River, surficial aquifers, and riparian wetlands.

Washington↗