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Aquatic ecology of the Elwha River estuary prior to dam removal: Chapter 7 in Coastal habitats of the Elwha River, Washington--biological and physical patterns and processes prior to dam removal

The removal of two long-standing dams on the Elwha River in Washington State will initiate a suite of biological and physical changes to the estuary at the river mouth. Estuaries represent a transition between freshwater and saltwater, have unique assemblages of plants and animals, and are a critical habitat for some salmon species as they migrate to the ocean. This chapter summarizes a number of studies in the Elwha River estuary, and focuses on physical and biological aspects of the ecosystem that are expected to change following dam removal. Included are data sets that summarize (1) water chemistry samples collected over a 16 month period; (2) beach seining activities targeted toward describing the fish assemblage of the estuary and migratory patterns of juvenile salmon; (3) descriptions of the aquatic and terrestrial invertebrate communities in the estuary, which represent an important food source for juvenile fish and are important water quality indicators; and (4) the diet and growth patterns of juvenile Chinook salmon in the lower Elwha River and estuary. These data represent baseline conditions of the ecosystem after nearly a century of changes due to the dams and will be useful in monitoring the changes to the river and estuary following dam removal.

Washington

Reconnaissance of contaminants in selected wastewater-treatment-plant effluent and stormwater runoff entering the Columbia River, Columbia River Basin, Washington and Oregon, 2008-10

Toxic contamination is a significant concern in the Columbia River Basin in Washington and Oregon. To help water managers and policy makers in decision making about future sampling efforts and toxic-reduction activities, a reconnaissance was done to assess contaminant concentrations directly contributed to the Columbia River through wastewater-treatment-plant (WWTP) effluent and stormwater runoff from adjacent urban environments and to evaluate instantaneous loadings to the Columbia River Basin from these inputs. Nine cities were selected in Oregon and Washington to provide diversity in physical setting, climate characteristics, and population density—Wenatchee, Richland, Umatilla, The Dalles, Hood River, Portland, Vancouver, St. Helens, and Longview. Samples were collected from a WWTP in each city and analyzed for anthropogenic organic compounds, pharmaceuticals, polychlorinated biphenyls (PCBs), polybrominated diphenyl ether (PBDEs [brominated flame-retardants]), organochlorine or legacy compounds, currently used pesticides, mercury, and estrogenicity. Of the 210 compounds analyzed in the WWTP-effluent samples, 112 (53 percent) were detected, and the detection rate for most compound classes was greater than 80 percent. Despite the differences in location, population, treatment type, and plant size, detection frequencies were similar for many of the compounds detected among the WWTPs. By contrast, the occurrence of polycyclic aromatic hydrocarbons (PAHs) was sporadic, and PCBs were detected at only three WWTPs. The stormwater-runoff samples were analyzed for a slightly different set of contaminants, with the focus on those expected to be related to road and land runoff—PCBs, PBDEs, organochlorine compounds, PAHs, currently used pesticides, trace elements, mercury, and oil and grease. A complex mixture of compounds was detected in stormwater runoff, with detections of 114 (58 percent) of the 195 compounds analyzed. The detection patterns and concentrations measured in the stormwater-runoff samples, however, were more heterogeneous than in the WWTP-effluent samples. This reflects differences in various factors, including suspended-sediment concentrations and known contamination sources present in some watersheds. Trace elements and PAHs, which are related to automobiles and impervious surfaces, were the most widespread compound classes detected in stormwater runoff, a typical finding in stormwater runoff in urban areas. With a better understanding of the presence of these contaminants in the environment, future work can focus on developing research to characterize the effects of these contaminants on aquatic life and prioritize toxic-reduction efforts for the Columbia River Basin.

Washington;Oregon

Geology of tight oil and potential tight oil reservoirs in the lower part of the Green River Formation, Uinta, Piceance, and Greater Green River Basins, Utah, Colorado, and Wyoming

The recent successful development of a tight oil play in the Eocene-age informal Uteland Butte member of the lacustrine Green River Formation in the Uinta Basin, Utah, using modern horizontal drilling and hydraulic fracturing techniques has spurred a renewed interest in the tight oil potential of lacustrine rocks. The Green River Formation was deposited by two large lakes, Lake Uinta in the Uinta and Piceance Basins and Lake Gosiute in the Greater Green River Basin. These three basins contain the world’s largest in-place oil shale resources with recent estimates of 1.53 trillion, 1.33 trillion, and 1.44 trillion barrels of oil in place in the Piceance, Uinta, and Greater Green River Basins, respectively. The Uteland Butte member was deposited during an early freshwater stage of the lake in the Uinta Basin prior to deposition of the assessed oil shale intervals. This report only presents information on the early freshwater interval and overlying brackish-water interval in all three basins because these intervals are most likely to have tight oil potential. Burial histories of the three basins were reconstructed to study (1) variations in subsidence and lake development, and (2) post deposition burial that led to the development of a petroleum system in only the Uinta Basin. The Uteland Butte member is a successful tight oil play because it is thermally mature for hydrocarbon generation and contains organic-rich shale, brittle carbonate, and porous dolomite. Abnormally high pressure in parts of the Uteland Butte is also important to production. Variations in organic richness of the Uteland Butte were studied using Fischer assay analysis from oil shale assessments, and pressures were studied using drill-stem tests. Freshwater lacustrine intervals in the Piceance and Greater Green River Basins are immature for hydrocarbon generation and contain much less carbonate than the Uteland Butte member. The brackish-water interval in the Uinta Basin is thermally mature for hydrocarbon generation but is clay-rich and contains little carbonate, and thus is a poor prospect for tight oil development.

Colorado, Utah, Wyoming

Deep aquifer recharge in the Columbia River Basalt Group, upper Umatilla River Basin, northeastern Oregon

Groundwater is an important component of the water resources of the upper Umatilla River Basin of northeastern Oregon. As such, understanding the capacity of the resource is vital. Past studies have estimated recharge in the study area. One recent study of the upper Umatilla River Basin indicated that about 80 percent of recharge entering the groundwater system is discharged to streams in the study area through shallow groundwater-flow paths, leaving about 20 percent of recharge to infiltrate deeper parts of the aquifer system. The purpose of this work is to quantify the spatial distribution and variability of deep aquifer recharge in the study area and to understand the reasons for a relatively low percentage of total recharge reaching the deeper parts of the groundwater-flow system. The study area is divided into two distinct physiographic regions—the highly dissected Blue Mountains and the lowland plains. Underlying both regions of the study area are basalts of the Columbia River Basalt Group (CRBG), which is the principal aquifer in the study area. Deep incision by streams in the Blue Mountains disrupts the lateral continuity of the CRBG aquifer units, and infiltrating water is more readily diverted laterally and discharged to streams and springs. In the lowland plains, incision is less pronounced. The shallow CRBG units might be disrupted, but deeper aquifer units retain their lateral continuity and enable groundwater to infiltrate deeper and flow laterally farther downgradient before discharging. Recharge to the deep basalt aquifers is estimated as the difference between total recharge and base flow. Total recharge is the portion of precipitation and applied irrigation water that infiltrates past the root zone to become groundwater recharge. Of this total recharge, a proportion discharges to springs and streams in the study area, and the remaining water infiltrates below the base level of streams and recharges the deep basalt aquifers and contributes to the regional groundwater flow system. The portion of total recharge that recharges the regional flow system is referred to as deep aquifer recharge. Total recharge is the portion of precipitation and applied irrigation water that infiltrates past the root zone to become groundwater recharge. It is the sum of recharge from precipitation and recharge from infiltration of irrigation water. Recharge from precipitation was calculated using a regression method developed for the Columbia Plateau. Recharge from infiltrating irrigation water was obtained from a water balance model developed for the Columbia Plateau. Base flow, the component of streamflow that represents groundwater discharge as opposed to runoff from the land surface, was estimated using the Base Flow Index Modified (BFI-Modified) method, an empirical hydrograph separation technique. Base flow was estimated in eight subbasins with streamgages within the study area. Five of the eight subbasins in which base flow was estimated had permitted water rights for irrigation that specified surface water as the primary source of water. Maximum surface-water withdrawal for irrigation was estimated for all subbasins in which water rights for irrigation occur. The base-flow estimate from BFI-Modified is assumed to be the minimum amount of base flow. The sum of the BFIModified base-flow estimate and the maximum permitted surface-water withdrawal estimate for each subbasin is assumed to be the maximum amount of base flow at the streamgage. These minimum and maximum estimates of base flow were used to calculate minimum and maximum values of deep aquifer recharge in each subbasin analyzed within the study area. Subbasin estimates were scaled up to the Blue Mountains and lowland plains regions, and to the entire study area. Mean annual total recharge for 1981–2010 in the subbasins, analyzed as part of this work, ranged from 6 inches (in.) in the Patawa and Wildhorse Creek subbasins in the lowland plains to as much as 20 in. in the Umatilla River above Meacham Creek subbasin. Mean annual total recharge totaled 4 in. in the lowland plains region and 14 in. in the Blue Mountains. Mean annual total recharge for the entire study area was 11 in. Mean annual base flow ranged from 1 in. in the Patawa and Wildhorse Creek subbasins in the lowland plains to as much as 14 in. in the Umatilla River above Meacham Creek subbasin in the Blue Mountains. Mean annual deep aquifer recharge ranged from 4 in. in the Patawa and Wildhorse Creek subbasins in the lowland plains to as much as 8 in. in the Isqu’ulktpe Creek subbasin in the Blue Mountains. Deep aquifer recharge was 3–4 in. in the lowland plains region and 6 in. in the Blue Mountains. Over the entire study area, mean annual deep aquifer recharge was 5 in. Most groundwater recharge (both total and deep aquifer) in the study area occurred in the Blue Mountains, which highlights the importance of the Blue Mountains as the principal source of groundwater for the study area and for aquifers farther downgradient. Total recharge in the Blue Mountains region represents 86 percent of the mean annual total recharge in the study area in an area that encompasses 65 percent of the study area. However, only 43–44 percent of the mean annual total recharge remains in the system to recharge the deeper, regional aquifer system because the rest is discharged as base flow within the Blue Mountains region. Within the lowland plains region of the study area, an estimated 67–84 percent of the mean annual total recharge remains in the system to recharge the deep, regional aquifer system. Although total recharge in the study area represents only 14 percent of the total recharge across the study area, it contributes 20–24 percent of the water to the deep aquifer. The difference in the percentage of deep groundwater recharge in the Blue Mountains and the lowland plains is attributed to differences in the degree of stream incision. Stream channels are more incised in the Blue Mountains region than they are in the lowland plains. The dissection of the landscape in the Blue Mountains disrupts the lateral continuity of the CRBG aquifer units and allows groundwater to discharge to springs and streams rather than infiltrate more deeply. In the lowland plains region, incision is much less pronounced and deeper CRBG units likely retain their lateral continuity, enabling groundwater to infiltrate more deeply than in the Blue Mountains.

Oregon

Characterization of water quality, biology, and habitat of the Pearl River and selected tributaries contiguous to and within Tribal lands of the Pearl River Community of the Mississippi Band of Choctaw Indians, 2017–18

The U.S. Geological Survey, in cooperation with the Mississippi Band of Choctaw Indians (MBCI), conducted a baseline assessment of the physical, chemical, and biological quality of selected streams and rivers within and contiguous to the Pearl River Community (PRC) in 2017 and 2018. The MBCI is a federally recognized tribe with territories in Mississippi and Tennessee. MBCI Tribal government and communities have sovereign authority over their natural resources and are responsible for protecting the quality of waters within the Tribal lands from sources of pollution and restoring impaired waters. The quality of these surface waters has a profound effect upon the health and welfare of MBCI Tribal members. Data generated from this study may be used with other relevant water-quality data for comparison and development of Tribal water-quality standards. The PRC territory is drained by the Pearl River and associated tributaries. Water-quality and biological samples were collected and habitat surveys were conducted at sites on the mainstem of the Pearl River and major tributaries of the Pearl River—Wolf Creek, Beasha Creek, Jones Creek, and Kentawka Creek. The selected stream sites represent a range of land use/land cover and potential sources of alteration and contamination from within their respective drainage areas. In particular, Wolf Creek watershed has the highest relative percentage of developed land. Ambient physicochemical properties, major ions, nutrients, and organic wastewater compounds (OWCs) were analyzed quarterly from surface-water samples from October 2017 through August 2018. Physicochemical properties were also measured in June 2018 over a continuous 48-hour period. Trace elements and polycyclic aromatic hydrocarbons were analyzed from streambed sediments in August 2018. Biological samples included the collection of periphyton algae (August 2018), benthic macroinvertebrate (March 2017 and March 2018), and fish communities (April 2018). Physical stream habitat characteristics were assessed using qualitative (March 2017 and March 2018) and quantitative surveys (August 2018). While not directly applicable, the State of Mississippi Water Quality Standards were used as reference to evaluate Tribal water quality. Physicochemical water-quality constituents—water temperature, specific conductance (SC), pH, and dissolved oxygen (DO)—were generally within natural ranges among sites and samples, with a few exceptions that exceeded existing Mississippi water-quality standards. pH and DO periodically were below the minimum State standards at some sampled sites. Specific conductance was also relatively high at both Wolf Creek sites but did not exceed the existing maximum standard for recreational waters. The surface water among stream sites was predominantly calcium bicarbonate type, with a shift toward sodium-bicarbonate water type at the downstream Wolf Creek (Wolf DS) site. Major ion concentrations were generally highest at the Wolf Creek sites. Nutrient concentrations were also often highest at Wolf DS, but total nitrogen and total phosphorus periodically exceeded recommended State and Federal nutrient criteria thresholds among most sampled sites. Twenty-nine OWCs, including 10 known or suspected endocrine disruptors, were detected among sites. Concentrations of OWCs were relatively low, and only 19 percent of all detections were above the reporting level. Concentrations of copper and nickel in streambed sediments were detected above consensus-based threshold-effect concentrations (TECs) at one site each, and arsenic and chromium exceeded TECs at most sites. Concentrations of all polycyclic aromatic hydrocarbons in streambed sediments were low and well below TECs at all sites. The periphyton, macroinvertebrate, and fish communities at most sampled sites appear typical of central Mississippi streams; however, the diversity, composition, and abundance of taxa sampled from Wolf DS were particularly distinctive compared to other sampled stream sites. Periphyton taxa richness was low at both Wolf Creek sites, and both sites had greater abundances of diatom taxa, which are indicative of high nutrient concentrations, than of soft-algae taxa. Similarly, Wolf DS had relatively low macroinvertebrate diversity, the fewest Ephemeroptera, Plecoptera, and Trichoptera taxa, a high abundance of Tubificid taxa, and the lowest overall Mississippi-Benthic Index of Stream Quality score. Fish species richness was also relatively low at Wolf DS compared to some other sampled sites. Habitat characteristics also appeared to be generally typical of most central Mississippi streams. Qualitative habitat assessment scores were at or above the regional least disturbed streams for Wolf DS, the upstream Wolf Creek (Wolf US) site, and Jones Creek. Habitat scores among the remaining sites indicate fair conditions. Quantitative and qualitative habitat characteristics indicate relatively lower habitat quality at the two Beasha Creek sites.

Mississippi

Sources of metal loads to the Alamosa River and estimation of seasonal and annual metal loads for the Alamosa River basin, Colorado, 1995-97

Metal contamination in the upper Alamosa River Basin has occurred for decades from the Summitville Mine site, from other smaller mines, and from natural, metal-enriched acidic drainage in the basin. In 1995, the need to quantify contamination from various source areas in the basin and to quantify the spatial, seasonal, and annual metal loads in the basin was identified. Data collection occurred from 1995 through 1997 at numerous sites to address data gaps. Metal loads were calculated and the percentages of metal load contributions from tributaries to three risk exposure areas were determined. Additionally, a modified time-interval method was used to estimate seasonal and annual metal loads in the Alamosa River and Wightman Fork. Sources of dissolved and total-recoverable aluminum, copper, iron, and zinc loads were determined for Exposure Areas 3a, 3b, and 3c. Alum Creek is the predominant contributor of aluminum, copper, iron, and zinc loads to Exposure Area 3a. In general, Wightman Fork was the predominant source of metals to Exposure Area 3b, particularly during the snowmelt and summer-flow periods. During the base-flow period, however, aluminum and iron loads from Exposure Area 3a were the dominant source of these metals to Exposure Area 3b. Jasper and Burnt Creeks generally contributed less than 10 percent of the metal loads to Exposure Area 3b. On a few occasions, however, Jasper and Burnt Creeks contributed a substantial percentage of the loads to the Alamosa River. The metal loads calculated for Exposure Area 3c result from upstream sources; the primary upstream sources are Wightman Fork, Alum Creek, and Iron Creek. Tributaries in Exposure Area 3c did not contribute substantially to the metal load in the Alamosa River. In many instances, the percentage of dissolved and/or total-recoverable metal load contribution from a tributary or the combined percentage of metal load contribution was greater than 100 percent of the metal load at the nearest downstream site on the Alamosa River. These data indicate that metal partitioning and metal deposition from the water column to the streambed may be occurring in Exposure Areas 3a, 3b, and 3c. Metals that are deposited to the streambed probably are resuspended and transported downstream during high streamflow periods such as during snowmelt runoff and rainfall runoff. Seasonal and annual dissolved and totalrecoverable aluminum, copper, iron, and zinc loads> for 1995?97 were estimated for Exposure Areas 1, 2, 3a, 3b, and 3c. During 1995?97, many tons of metals were transported annually through each exposure area. Generally, the largest estimated annual totalrecoverable metal mass for most metals was in 1995. The smallest estimated annual total-recoverable metal mass was in 1996, which also had the smallest annual streamflow. In 1995 and 1997, more than 60 percent of the annual total-recoverable metal loads generally was transported through each exposure area during the snowmelt period. A comparison of the estimated storm load at each site to the corresponding annual load indicated that storms contribute less than 2 percent of the annual load at any site and about 5 to 20 percent of the load during the summer-flow period.

Colorado

Review of Selected References and Data sets on Ambient Ground- and Surface-Water Quality in the Metedeconk River, Toms River, and Kettle Creek Basins, New Jersey, 1980-2001

Surface water and ground water from unconfined aquifers are the primary sources of drinking water for much of the population, about 391,000, in the Metedeconk River, Toms River, and Kettle Creek watersheds in the New Jersey Coastal Plain. The quality of these sources of drinking water is a concern because they are vulnerable to contamination. Indications of the occurrence, distribution, and likely sources and transport mechanisms of certain contaminants were obtained from 48 selected reports and 2 selected data sets on water quality in or near the watersheds (1980-2001). These indications are described and briefly summarized in this report. The findings of studies on ground-water quality indicate that shallow ground water within the study area generally meets primary drinking-water standards, with notable exceptions. Volatile organic compounds, mercury, arsenic, radionuclides, nitrate, and coliform bacteria have been detected in shallow ground water in some areas at levels that exceed Federal and State drinking-water standards. For example, results of analyses of untreated samples collected from more than 13,000 private wells during 1983-99 indicated that concentrations of volatile organic compounds in samples from 7.3 percent of the wells exceeded at least 1 of 11 drinking-water standards, according to records maintained by the Ocean County Health Department. In cases of exceedances, however, water treatment, well replacement, and (or) retesting assured that applicable drinking-water standards were being met at the tap. Reported concentrations of the pesticide chlordane in some areas exceeded the drinking-water standard; few data are available on the occurrence of other pesticides. Studies of nearby areas, however, indicate that pesticide concentrations generally could be expected to be below drinking-water standards. The combination of low pH and low dissolved solids in many areas results in shallow ground water that is highly corrosive and, if untreated, able to leach trace elements and release asbestos fibers from plumbing materials. Reported concentrations of nitrate, volatile organic compounds, trace elements, and pesticides in samples from the monitored mainstem and tributary streams within the study area generally are below maximum contaminant levels for drinking water or below detection limits. Results of studies in other areas indicate that pesticide concentrations in surface water could be considerably higher during high flows soon after the application of pesticides to crops than during low flows. Fecal coliform bacteria counts in streams vary considerably. Concentrations or counts of these classes of surface-water-quality constituents likely are functions of the intensity and type of upstream development. Results of limited monitoring for radionuclide concentrations reported by the Brick Township Municipal Utilities Authority of the Metedeconk River indicate that radionuclide concentrations or activities do not exceed maximum contaminant levels for drinking water. As a consequence of organic matter in surface water, the formati ultraviolet absorbance in samples from the Metedeconk River and the Toms River exceeded the alternative compliance criteria for source water (2.0 milligrams per liter for total organic carbon and 0.02 absorbance units-liters per milligram-centimeter for specific ultraviolet absorbance) with respect to treatment requirements for preventing elevated concentrations of disinfection by-products in treated water. Water-quality and treatment issues associated with use of ground and surface water for potable supply in the study area are related to human activities and naturally occurring factors. Additional monitoring and analysis of ground and surface water would be needed to determine conclusively the occurrence and distribution of some contaminants and the relative importance of various potential contaminant sources, transport and attenuation mechanisms, and transport pathways.

Water-Resources Investigations Report

Flow routing in the Susquehanna River Basin: Part I - Effects of Raystown Lake on the low-flow frequency characteristics of the Juniata and lower Susquehanna Rivers, Pennsylvania

A flow-routing model was used to simulate 17 water years of daily streamflows at five sites. The sites were Mapleton Depot and Newport, Pennsylvania, on the Juniata River, and Harrisburg and Marietta, Pennsylvania, and Conowingo, Maryland, on the Susquehanna River. The purpose for the simulations was to determine the effects of a new reservoir, Raystown Lake, on the low-flow frequency characteristics of these sites. Raystown Lake is on Raystown Branch Juniata River, a tributary to the Juniata River. Output from a reservoir-regulation model of Raystown Lake was used as input to the flow-routing models. In addition, a reservoir-routing model was developed for the hydroelectric power dams on the lower Susquehanna River. Low-flow frequency curves, based on the post-Raystown Lake simulated flows, were compared to similar curves based on pre-Raystown observed data. The comparison indicated that operation of the lake will cause estimated increases in the 7-day 10-year low flows ranging from 420 cfs at Mapleton Depot to 290 cfs at Marietta and Conowingo over the 7-day 10-year low flows for pre-Raystown conditions. Although inherent modeling errors exist in all of these simulated data, the overall quality of the simulated flows and the low-flow frequency curves is considered good. (Woodard-USGS)

Pennsylvania

Flow routing in the Susquehanna River Basin: Part III -- Routing reservoir releases in the Tioga and Chemung rivers system, Pennsylvania, and New York, 1977

Channel-routing models were used to route hypothetical releases from reservoirs in the upper Tioga River basin, Pennsylvania. These releases were routed northward down the Tioga River to Lindley, Erwins, and Corning, New York: combined with flows routed down the Cohocton River from Campbell to Corning, New York; and then routed southeastward down the Chemung River from Corning to Chemung, New York. The models used to route the flows of Cohocton and Chemung Rivers accounted for bank-storage discharge and streamflow depletion by well pumpage. In general, 17 water years of concurrent streamflow data were available for model calibration and verification. Three hypothetical reservoir releases were made from the reservoirs and routed to Wilkes-Barre, Pennsylvania, using the models developed in this study and models developed downstream to Wilkes-Barre in a previous study. A hypothetical makeup water requirement of 65 cubic feet per second was assumed. Two historical low-flow periods were investigated. The first hypothetical release investigated was a constant 100 cubic feet per second, and the second release was a constant 70 cubic feet per second. The third scheme was a hypothetical release of 100 cubic feet per second for three days followed by a constant 70 cubic feet per second for the duration of the period considered. Constant 100 cubic feet per second releases arrived downstream more quickly than constant 70 cubic feet per second releases for both test periods, but delivered more water than required to satisfy the assumed makeup requirement. The third release scheme was generally the most efficient of the three schemes tested. Although inherent modeling errors exist in all the simulated data, the accuracy of the estimated routed reservoir releases at the downstream sites is considered good.

New York, Pennsylvania

Annual suspended-sediment loads in the Green River at Green River, Utah, 1930-82

The Green River above gaging station 093150000 at Green River, Utah, drains about 44,850 square miles in Utah, Colorado, and Wyoming. The average annual precipitation near the station was 6.11 inches. Rocks ranging in age from Precambrian to Holocene are exposed in the Green River drainage basin above Green River, Utah. Shale, siltstone, and mudstone of Tertiary age probably are the most easily eroded rocks in the basin, and they contribute a large part of the sediment load in the Green River. During 1930-82, the U.S. Geological Survey collected records of fluvial sediment at station 093150000. Based on these records the mean annual suspended-sediment load was about 15,630,000 tons, ranging from 1,780,000 tons during 1934 to 43,400,000 tons during 1937. The minimum daily load of 54 tons was on September 27, 1956, and the maximum daily load of 2,230,000 tons was on July 11, 1936. Analysis of the suspended-sediment records collected from 1930-82 at station 093150000 indicated that the accuracy of the records is fair prior to 1945 and good for the remaining period of record. The records after 1945 reflect the use of improved sampling equipment. (USGS)

Water-Resources Investigations Report

Heterogeneous detection probabilities for imperiled Missouri River fishes: implications for large-river monitoring programs

Occupancy modeling was used to determine (1) if detection probabilities (p) for 7 regionally imperiled Missouri River fishes (Scaphirhynchus albus, Scaphirhynchus platorynchus, Cycleptus elongatus, Sander canadensis, Macrhybopsis aestivalis, Macrhybopsis gelida, and Macrhybopsis meeki) differed among gear types (i.e. stationary gill nets, drifted trammel nets, and otter trawls), and (2) how detection probabilities were affected by habitat (i.e. pool, bar, and open water), longitudinal position (five 189 to 367 rkm long segments), sampling year (2003 to 2006), and season (July 1 to October 30 and October 31 to June 30). Adult, large-bodied fishes were best detected with gill nets (p: 0.02–0.74), but most juvenile large-bodied and all small-bodied species were best detected with otter trawls (p: 0.02–0.58). Trammel nets may be a redundant sampling gear for imperiled fishes in the lower Missouri River because most species had greater detection probabilities with gill nets or otter trawls. Detection probabilities varied with river segment for S. platorynchus, C. elongatus, and all small-bodied fishes, suggesting that changes in habitat influenced gear efficiency or abundance changes among river segments. Detection probabilities varied by habitat for adult S. albus and S. canadensis, year for juvenile S. albus, C. elongatus, and S. canadensis, and season for adult S. albus. Concentrating sampling effort on gears with the greatest detection probabilities may increase species detections to better monitor a population's response to environmental change and the effects of management actions on large-river fishes.

Endangered Species Research

Hyperspectral Image Transects during Transient Events in Rivers (HITTER): Framework development and application to a tracer experiment on the Missouri River, USA

Rivers convey a broad range of materials, such as sediment, nutrients, and contaminants. Much of this transport can occur during or immediately after an episodic, pulsed event like a flood or an oil spill. Understanding the flow processes that influence the motion of these substances is important for managing water resources and conserving aquatic ecosystems. This study introduces a new remote sensing framework for characterizing dynamic phenomena at the scale of a channel cross-section: Hyperspectral Image Transects during Transient Events in Rivers (HITTER). We present a workflow that uses repeated hyperspectral scan lines acquired from a hovering uncrewed aircraft system (UAS) to quantify how a water attribute of interest varies laterally across the river and evolves over time. Data from a tracer experiment on the Missouri River are used to illustrate the components of the end-to-end processing chain we used to quantify the passage of a visible dye. The framework is intended to be flexible and could be applied in a number of different contexts. The results of this initial proof-of-concept investigation suggest that HITTER could potentially provide insight regarding the dispersion of a range of materials in rivers, which would facilitate ecological and geomorphic studies and help inform management.

Remote Sensing

River channel response to the removal of the Pilchuck River Diversion Dam, Washington State

In August 2020, the 3-m tall Pilchuck River Diversion Dam was removed from the Pilchuck River, allowing free fish passage to the upper third of the watershed for the first time in over a century. The narrow, 300-m long impoundment behind the dam was estimated to hold 4,000–7,500 m 3 of sand and gravel, representing less than one year's typical bedload flux. Repeat cross section surveys, stage sensors, and time-lapse cameras were used to document the physical channel response over the first year following dam removal. A total of 7,400 m 3 (effectively 100%) of impoundment sediment was eroded in the first year, with 25% accomplished by manual regrading during dam removal. Most river-caused erosion occurred during a sequence of modest flows in October 2020. Downstream deposition totaled 4,300 m 3 , predominately filling in the first 100 m downstream of the dam site. Deposition tapered below detectable levels within 350 m, and most downstream channel adjustments occurred before November 2020. Multiple high flows after December 2020 caused little upstream or downstream change. The physical river response to this dam removal then appears to have been largely accomplished within several months by modest flows, consistent with pre-removal modeling and observations from other regional dam removals. Efficient sediment evacuation was likely aided by the narrow and steep-walled impoundment geometry. Our observations support existing guidance that the physical river response to small dam removals is typically rapid and modest; the benefits of removal may then often be gained with minimal negative downstream geomorphic impacts.

Washington

Environmental DNA (eDNA) surveillance of the federally threatened Slender Chub (Erimystax cahni) in the Clinch River and Powell River

The slender chub ( Erimystax cahni ) is a federally threatened fish native to and geographically restricted to eastern North America. More specifically, the Powell, Clinch, and lower Holston Rivers in Tennessee were historical collection areas. Habitat degradation from multiple sources, including surface mining, agriculture, dams, and urbanization, is associated with the decline of this species - an obligate inhabitant of gravel shoals in large rivers. As of 1964, only 15 voucher specimens were known and no living specimens were documented for decades. A federal recovery plan and Species Status Assessment were developed to determine if slender chub still exists and could be restored. Given the lack of recent observations using conventional sampling to search for its presence, we used environmental DNA sampling to determine their potential presence. Our specific objectives were to (1) develop a quantitative polymerase chain reaction (qPCR) assay aimed at species-specific detection and (2) sample historically known areas of collection. We sampled 43 sites in the Clinch and Powell Rivers. For the first time in almost two decades, we provide evidence for the continued existence of a putatively extinct species. We detected evidence of E. cahni in both the Clinch and Powell Rivers, but only at a few sites. We cannot confirm the presence of E. cahni , and positive eDNA matches could be attributed to amplification from a hybrid. Our results do indicate slender chub DNA perseveres in the Clinch and Powell Rivers and can inform resource agencies of localities to pursue on-the-ground searches for the slender chub with conventional methods (e.g., snorkeling) and potential restoration and recovery sites.

Tennessee, Virginia

Accuracy assessment/validation methodology and results of 2010–11 land-cover/land-use data for Pools 13, 26, La Grange, and Open River South, Upper Mississippi River System

Introduction/Background The U.S. Geological Survey (USGS)-Upper Midwest Environmental Sciences Center (UMESC) was responsible for development of several land cover/land use (LCU) systemic datasets of the Upper Mississippi River System (UMRS). These efforts (1989 and 2000) were funded by the U.S. Army Corps of Engineers’ Upper Mississippi River Restoration Program (UMRR) Long Term Resource Monitoring (LTRM) element. Development of systemic datasets includes the acquisition, processing, and serving of high-resolution aerial photography and land cover/land use spatial datasets ( http://www.umesc.usgs.gov/data_library/land_cover_use/land_cover_use_data.html ). In 2008, the UMRR reached a collaborative agreement with the U.S. Fish and Wildlife Service-Region 3 to collect high-resolution digital imagery of the entire UMRS floodplain during 2010–11 for LTRM. The UMESC helped acquire, process, and serve this imagery, as well as produce and serve the 2010–11 LCU systemic dataset of the UMRS floodplain. Digital imagery for Pools 13, 26, La Grange, and Open River South was collected using an Applanix DSS 439 digital sensor system with a 40 millimeter lens and Color Infrared (CIR) filter. The imagery was collected at a resolution of 20 centimeters/pixel (8 inches/pixel) for Pool 13 and 40 centimeters/pixel (16 inches/pixel) for Pools 26, Open River South, and La Grange. All imagery was projected to Universal Transverse Mercator (UTM) Zone 15, North American Datum of 1983 (NAD 83). The General Wetland Vegetation Classification (GWVC) system used for mapping is hierarchical, and its 31 classes can be collapsed into broader categories using either a 15- or 7-class level. While the 1989 and 2000 LCU systemic datasets have not gone through a traditional thematic accuracy assessment (AA) in the past, nor have they undergone a validation analysis, the end products are of high quality. For each systemic dataset produced (1989, 2000, 2010–11), extensive field reconnaissance is performed before photointerpretation. The intent of this field reconnaissance is to learn, test, and verify image signatures as they relate to vegetation types. Questionable areas on the imagery are visited, and the plants or land features observed in the area are recorded for reference. This procedure verifies vegetation signatures on the imagery with those on the ground. In addition, once the photointerpretation is complete, the final LCU dataset undergoes extensive quality assurance/quality control to ensure the imagery is mapped correctly. Since the 2000 LCU systemic dataset was developed, there has been a growing interest in completing thematic AAs for the LTRM LCU spatial datasets. The objective of an AA is to measure the probability that a particular location has been assigned its correct vegetation class. An AA estimates thematic (map class) errors in the data, giving users information needed to determine data suitability for a particular application. At the same time, data producers are able to learn more about the nature of errors in the data. Thus, the two attributes of an AA are “producers’ accuracy,” which is the probability that an AA point has been mapped correctly (also referred to as an error of omission); and “users’ accuracy,” which is the probability that the map actually represents what was found on the ground (also referred to as error of commission). Producers’ and users’ accuracies can be obtained from the same set of data by using different analyses. Accuracy assessment is an extensive effort that requires seasonal field personnel and equipment, data entry, analyses, and post processing—tasks that are costly and time consuming. The geospatial team at the UMESC has suggested a validation process for understanding the accuracy of the spatial datasets, which will be tested on at least some areas of the UMRS. Validation is not a true verification of map-class type in the field; however, it can provide the user of the map with useful information that is similar to a field AA. Similar to an AA, validation involves generating random points based on the total area for each map class. However, instead of collecting field data, two or three individuals not involved with the photo-interpretative mapping separately review each of the points onscreen and record a best-fit vegetation type(s) for each site. Once the individual analyses are complete, results are joined together and a comparative analysis is performed. The objective of this initial analysis is to identify areas where the validation results were in agreement (matches) and areas where validation results were in disagreement (mismatches). The two or three individuals then perform an analysis, looking at each mismatched site, and agree upon a final validation class. (If two vegetation types at a specific site appear to be equally prevalent, the validation team is permitted to assign the site two best-fit vegetation types.) Following the validation team’s comparative analysis of vegetation assignments, the data are entered into a database and compared to the mappers’ vegetation assignments. Agreements and disagreements between the map and validation classes are identified, and a contingency table is produced. This document presents the AA processes/results for Pools 13 and La Grange, as well as the validation process/results for Pools 13 and 26 and Open River South.

Iowa, Illinois, Minnesota, Missouri, Wisconsin

Columbia River Project water use plan: Mid Columbia River sturgeon incubation and rearing study (Year 1)

This report describes the results from the first year of a three-year investigation on the effects of different thermal regimes on incubation and rearing early life stages of white sturgeon. The Columbia River has been significantly altered by the construction of dams resulting in annual flows and water temperatures that differ from historical levels. White sturgeon have been demonstrated to spawn in two very distinct sections of the Columbia River in British Columbia, Canada, which are both located immediately downstream of hydropower facilities. The thermal regimes differ substantially between these two areas. The general approach of this study was to incubate and rear white sturgeon early life stages under two thermal regimes; one mimicking the current, cool water regime of the mid Columbia River downstream from Revelstoke Dam, and one mimicking a warmer regime similar to conditions found on the lower Columbia River at the international border. It describes the development of thermal profiles to be used in laboratory experiments from historic Columbia River temperature data. First-year results suggest that thermal regimes during incubation influence rate of egg development and size at hatch. Eggs incubated under the warm thermal regime hatched sooner than those incubated under the cool thermal regime. Mean length of free embryos at hatch was significantly different between thermal regimes with free embryos from the cool thermal regime being larger at hatch. However, free embryos from the warm thermal regime had a significantly higher mean weight at hatch. Mortality between hatch and initiation of feeding was extremely high in both treatments and virtually all fish reared under the warm thermal regime died prior to initiation of feeding. A proportion of the fish reared under the cool thermal regime did begin feeding; however, growth rates were extremely low as the onset of feeding corresponded with decreasing thermal regime temperatures. Chronic low levels of mortality resulted in few fish remaining when the growth trials were terminated at 154 days after egg fertilization. The starvation trials showed that the fish in the warm thermal regime exhausted their yolk reserves faster than fish in the cool thermal regime. The ability to resist starvation may be important in dispersal to downstream rearing areas.

British Columbia

Geologic map of the Dog River and northern part of the Badger Lake 7.5′ quadrangles, Hood River County, Oregon

The Dog River and northern part of the Badger Lake 7.5' quadrangles encompasses an area of ~201 km2 (77.6 mi2) of the High Cascades of north-central Oregon, lying across the eastern slopes of Mount Hood volcano (Figure 1-1; Plate 1; referred to herein as Dog River–Badger Lake area). Mount Hood, known as Wy’east to Native Americans, is Oregon’s tallest peak (3,427 m [11,241 ft]). The volcano has erupted episodically for the past 500,000 years, experiencing two major eruptive periods during the last 1,500 years (Scott and others, 1997a; Scott and others, 2003; Scott and Gardner, 2017). Cascade Range volcanism and structural development in the area dates back longer, with eruptive activity dating from latest Miocene to recent time; part of that volcano-tectonic record is detailed by new high-resolution geologic mapping presented here. The geology of the Dog River–Badger Lake area was mapped by the Oregon Department of Geology and Mineral Industries (DOGAMI) between 2017 and 2020, in collaboration with geoscientists from the U. S. Geological Survey Cascade Volcano Observatory (USGS CVO) and Hamilton College, New York. The primary objective of this investigation is to provide an updated and spatially accurate geologic framework for the Dog River–Badger Lake area as part of a multi-year study of the geology of the larger Middle Columbia Basin (Figure 1-1, Figure 1-2). Additional key objectives of this project are to: 1) determine the geologic history of volcanic rocks in this part of the northern Oregon Cascade Range, including lava flows and volcaniclastic deposits erupted from Middle Pleistocene to Holocene Mount Hood volcano; 2) provide significant new details about the structure and fault history along the northern segment of the High Cascades intra-arc graben (Hood River graben); and 3) better understand geologic hazards in the region, related to earthquakes, volcanoes, and landslides. New detailed geologic data presented here also provides a basis for future geologic, geohydrologic, and geohazard studies in the greater Middle Columbia Basin. Detailed geologic mapping in this part of the Middle Columbia Basin is a high priority of the Oregon Geologic Map Advisory Committee (OGMAC), supported in part by grants from the STATEMAP component of the USGS National Cooperative Geologic Mapping Program (G17AC00210, G19AC00160). Additional funds were provided by the State of Oregon. The core products of this study are this report, an accompanying geologic map and cross sections (Plate 1), an Esri ArcGIS™ geodatabase, and Microsoft Excel® spreadsheets tabulating point data for geochemistry, geochronology, magnetic polarity, orientation points, and well data. The geodatabase presents the new geologic mapping in a digital format consistent with the USGS National Cooperative Geologic Mapping Program Geologic Map Schema (GeMS) (U.S. Geological Survey National Cooperative Geologic Mapping Program, 2020). This geodatabase contains spatial information, including geologic polygons, contacts, structures, geochemistry, geochronology, magnetic observation, orientation points, and well data, as well as data about each geologic unit such as age, lithology, mineralogy, and structure. Digitization at scales of 1:8,000 or better was accomplished using a combination of high-resolution lidar topography and imagery. Surficial and bedrock geologic units contained in the geodatabase are depicted on the Plate 1 at a scale of 1:24,000. Both the geodatabase and geologic map are supported by this report describing the geology in detail.

Oregon

Occupancy rates of river otters (Lontra canadensis) in the St. Louis River Area of Concern

The St. Louis River Area of Concern (AOC), an estuarine system along the northeastern Minnesota-Wisconsin border, experienced significant ecological disturbances and degradation from unregulated industrial development during the 19 th and 20 th centuries. Recent restoration and remediation efforts in the AOC have led to substantial improvements in water quality, habitat, and fisheries populations. However, the status of wildlife populations following restoration efforts in the AOC remain largely unknown. We used remote cameras to estimate occupancy rates of river otters Lontra canadensis in the AOC and at two reference areas that had not been subjected to historical degradation. Because river otters occupy a high trophic level within these systems, we hypothesized that they would be an effective indicator species of overall habitat quality and recovery. Using data collected from June 2015 to February 2016, we developed single-season occupancy models for both summer and winter seasons. We found no differences in occupancy between the AOC and the reference sites, suggesting that river otter populations within the AOC were comparable to those in unaffected areas. Our results indicate that habitat restoration and remediation efforts in the St. Louis River estuary have been successful in promoting healthy wildlife populations.

Minnesota, Wisconsin