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USGS2022

Wind River subbasin restoration: Annual Report of U.S. Geological Survey activities January 2020 through December 2020

We sampled juvenile wild Steelhead Trout Oncorhynchus mykiss in headwater streams of the Wind River, WA, to characterize population attributes and investigate life-history metrics, particularly migratory patterns, and early life-stage survival. We used passive integrated transponder (PIT) tagging and a series of instream PIT-tag interrogation systems (PTISs) to track juveniles and adults. The Wind River subbasin is considered a wild Steelhead refuge by Washington Department of Fish and Wildlife (WDFW). No hatchery Steelhead Trout have been released in the Wind River subbasin since 1997, and hatchery adults are estimated at less than one percent of spawners in most years. Over twenty years of Steelhead Trout status and trend monitoring and research in the subbasin is contributing to understanding of population response to numerous restoration actions in the subbasin, including removal of Hemlock Dam from Trout Creek in 2009, which had an outdated adult ladder and contributed to increased water temperatures reducing performance of juvenile Steelhead Trout. Data from our study, and companion work by Washington Department of Fish and Wildlife, are contributing to Bonneville Power Administration’s (BPA) Research, Monitoring, and Evaluation (RM&E) Program Strategy of Fish Population Status Monitoring (https://www.cbfish.org/ProgramStrategy.mvc/Index). Specifically, this work addresses the substrategies of 1) Assessing the Status and Trends of Diversity of Natural Origin Fish Populations and Uncertainties Research regarding differing life histories of a wild Steelhead Trout population, 2) Assessing the Status and Trend of Adult Natural Origin Fish Populations, and 3) Monitoring and Evaluating the Effectiveness of Tributary Habitat Actions Relative to Environmental, Physical, or Biological Performance Objectives. During summer and fall 2020, we PIT-tagged 1,415 Steelhead parr (age-0 and age-1) in the Trout Creek and upper Wind River watersheds. Recaptures and detections of PIT-tagged Steelhead Trout parr happened through repeat headwater sampling, smolt trap operations, and instream PTISs and Columbia River PIT-tag detection infrastructure. Throughout the year, we maintained a series of six instream PTISs to monitor movement of tagged Steelhead Trout parr, smolts, and adults, providing data to population assessments, and life-cycle research and modeling. Detection data from PIT-tagged adult Steelhead Trout at PTISs allow assessment of adult escapement to tributary watersheds within the Wind River subbasin. Adult Steelhead Trout detection efficiency estimates at our primary PTIS in Trout Creek have been greater than 92 percent during eight of the past nine years and have exceeded 90% at our primary PTIS in the Wind River the past three years. Adult escapement estimates to tributary watersheds are helping evaluate the efficacy of the 2009 removal of Hemlock Dam from rkm 2.0 of Trout Creek. The dam had potential negative effects on Steelhead Trout populations in Trout Creek due to hydrologic impairment, increased temperatures, and adult passage issues. Hemlock Dam was laddered for adult passage, but not to modern standards, which likely resulted in avoidance by some adult Steelhead Trout. We continue to improve our PTISs in the Wind River subbasin. The improvements in siting and addition of grid power to the upper Wind River PTIS (site code WRU, rkm 27.6) during 2016 and 2017, and the addition of the Mine Reach site (site code MIN, rkm 36.0) have much improved PIT-tagged fish monitoring in the upper Wind River watershed. The paired PTIS design in the upper Wind River watershed (sites WRU and MIN), matches that in the Trout Creek watershed (sites TRC and TC4) and will allow comparisons of Steelhead Trout population metrics between the two watersheds as response to Hemlock Dam removal continues and future restoration efforts occur in Trout Creek. We installed two new PTISs during 2020. Both were installed downstream of our primary interrogation sites on Trout Creek and in the mainstem Wind River. We hope the two new sites will provide interrogations information that will allow us to better estimate detection efficiencies of downstream moving juvenile Steelhead Trout at the primary interrogation sites. The additional interrogations will be particularly important for those fish tagged with 9-mm PIT tags as less information from downstream locations is available from them. These sites and other status and trend data will allow evaluation of further planned restoration within the watershed, particularly that proposed for the headwaters of Trout Creek. Detections at the instream PTISs have demonstrated trends of age-0 and age-1 parr emigration from natal areas during summer and fall, in addition to the expected movement of parr and smolts in spring. We have estimated that from 15 to 51% of parr tagged as age-0 fish in headwater areas make downstream migrations at age 1 for additional rearing during both spring and fall. We have estimated that up to 27% of Steelhead Trout parr, tagged as age-1 fish, make downstream migrations during fall. These findings raise questions about where parr most successfully rear and whether migrations are density or habitat quality driven. Broader monitoring programs would give a more comprehensive understanding of juvenile Steelhead Trout production and rearing and productivity contribution. Repeat sampling at consistent locations in the subbasin has enabled assessment of juvenile Steelhead Trout growth patterns. Growth rates (relative change in weight) of age-0 PITtagged parr during summer were similar across the subbasin but lower for age-1 parr in the Trout Creek watershed than the upper Wind River watershed. Yearly relative growth for parr tagged at age-0 is similar across the subbasin. Non-native Brook Trout Salvelinus confluentus are present in the subbasin, chiefly the Trout Creek watershed, and repeat sampling has allowed us to index their prevalence. Mean percent-of-catch that is Brook Trout, at four sample sites in Trout Creek, has declined from the period 1998 – 2003 to the period 2011 – 2020. Percent-of-catch and number of Brook Trout at the Trout Creek sites from 2011 through 2020 declined, though both metrics increased in 2018. Evaluation and planning of restoration efforts are critical to ensure efficient use of resources. Assessing Steelhead Trout life history variation in the Wind River subbasin will inform research and tracking of many populations and help inform habitat restoration and water allocation planning. Movement of Steelhead Trout parr from natal areas to other rearing areas raises questions regarding juvenile abundance, origin, and habitat use within watersheds. Improved PTISs and focused PIT tagging of age-0 and age-1 Steelhead Trout parr allow investigation of such questions. Increasingly detailed viable salmonid population information, such as that provided by PIT-tagging and instream PTIS networks like those in the Wind River can provide data to inform fisheries policy and management and understand life-history strategies and limiting factors. Such efforts also provide assessment of long-term effects of habitat restoration actions such as the removal of Hemlock Dam on Trout Creek, and the proposed Stage-0 restoration effort for upper Trout Creek, which would be a large-scale effort to reset sections of stream within their floodplain, restoring connectivity and interaction with surrounding landscape.

Washington↗

USGS2026

Wind River subbasin restoration: Annual report of U.S. Geological Survey activities January 2024 through December 2024

We sampled juvenile wild Oncorhynchus mykiss (Steelhead Trout) in headwater streams of the Wind River, Washington, to characterize population attributes and investigate life-history metrics, particularly migratory patterns, and early life-stage survival. Additionally, this sampling provides an index of abundance of non-native Brook Trout Salvelinus confluentus . We used passive integrated transponder (PIT) tagging and a series of instream PIT-tag interrogation systems (PTISs) to track juveniles and adults. The Wind River subbasin is considered a wild Steelhead refuge by Washington Department of Fish and Wildlife (WDFW). No hatchery Steelhead Trout have been released in the Wind River subbasin since 1997, and hatchery adults are estimated at less than one percent of spawners in most years. Over 25 years of Steelhead Trout status and trend monitoring and research in the subbasin is contributing to understanding of population response to numerous restoration actions in the subbasin, including removal of Hemlock Dam from Trout Creek in 2009, which had an inadequate adult ladder and contributed to increased water temperatures, to near lethal levels for salmonids. Data from our study, and companion work by WDFW, are contributing to the Columbia Basin Fish and Wildlife Program (2009) Research, Monitoring, and Evaluation (RM&E) Strategy of Fish Population Status Monitoring. Specifically, this work addresses the sub-strategies of 1) Assessing the Status and Trends of Diversity of Natural Origin Fish Populations and Uncertainties Research regarding differing life histories of a wild Steelhead Trout population, 2) Assessing the Status and Trend of Adult Natural Origin Fish Populations, and 3) Monitoring and Evaluating the Effectiveness of Tributary Habitat Actions Relative to Environmental, Physical, or Biological Performance Objectives. During summer and fall 2024, we PIT-tagged 2,075 Steelhead Trout parr (age-0 and age-1), in the Trout Creek and upper Wind River watersheds. Age-0 and age-1 parr were at high abundance due to strong spawner numbers in 2023 and 2024 (Estimate of 932 in 2023; and a moderate number of spawners in 2024 though an estimate is not available at this time; 24-year median = 619; Charlie Cochran, WDFW Fish Biologist, personal commun., 2025). An additional 100 parr (age-0 and age-2 or older) were tagged to provide fish for estimating detection efficiencies at PTISs. Steelhead Trout parr were recaptured and detected through repeat headwater sampling, smolt trapping, instream PTISs and Columbia River mainstem PIT-tag detection. We maintained and upgraded six instream PTISs to detect PIT-tagged Steelhead Trout parr, smolts, and adults, providing data for population assessments, and life-cycle research. Detection data from PIT-tagged adult Steelhead Trout at our four primary PTISs allow assessment of adult escapement to tributary watersheds within the Wind River subbasin. Most adult Steelhead detected were tagged by WDFW at an adult trap in the lower Wind River and some as smolts at screw traps. Adult Steelhead Trout detection efficiency estimates at our primary PTIS in Trout Creek have been greater than 99 percent during eight of the past ten years and have exceeded 97% at our primary PTIS in the Wind River during nine of the past ten years. Adult escapement estimates to tributary watersheds are helping evaluate the efficacy of the 2009 removal of Hemlock Dam from rkm 2.0 of Trout Creek. Detections at the instream PTISs have shown trends of age-0 and age-1 Steelhead Trout parr emigration from natal areas during summer and fall, in addition to the expected movement of parr and smolts in spring. Our data suggest that most fish from a cohort that migrate downstream will do so at age-1 for additional rearing in the subbasin. We have estimated that from 15% to 56% of parr tagged as age-0 fish in headwater areas make downstream migrations at age-1 for additional rearing (median = 29%). We have estimated that from 1% to 27% of Steelhead Trout parr, tagged as age-1 fish, make downstream migrations during fall (median = 3.5%): this is especially pronounced in the upper Wind River portion of the watershed (median 10%). These findings raise questions about parr rearing habitat and whether migrations are density- or habitat-quality driven, and answers to such questions are long-term goals of this study as active and passive habitat restoration occurs. Repeat sampling at sites in the subbasin within and between years has enabled assessment of juvenile Steelhead Trout growth patterns. Growth rates (relative change in weight) of age-0 PIT-tagged parr during summer have been similar across the subbasin, though slightly lower in the Trout Creek watershed (Trout Creek sites, 0.57 - 1.25%/day, Wind River sites = 0.94 – 2.48%/day). Summer growth rates have been lower for age-1 parr in the Trout Creek watershed than the upper Wind River watershed (Trout Creek sites, = 0.03 - 0.14%/day, Wind River sites = 0.05 – 0.19%/day). Yearly relative growth was similar across the subbasin for both age-0 and age-1 tagged parr. During 2024 range of mean daily relative change in weight from the previous year for age-0 tagged fish was: Trout Creek sites = 0.96 – 1.41%/day, Wind River sites = 0.80 – 1.30 %/day; and for age1 tagged fish was: Trout Creek sites = 0.37 - 0.50 %/day, Wind River sites = no age-1 tagged recaptures. Non-native Brook Trout are present in the subbasin, chiefly the Trout Creek watershed. Mean percent-of-catch that is Brook Trout, at four sample sites in Trout Creek, has declined from the period 1998 – 2003 to the period 2011 – 2024 (range of decrease = 19 - 82%). Percent-of-catch (of 64 samples, 52 < 10%; 3 > 20%) and number of Brook Trout at the Trout Creek sites from 2011 through 2024, though variable, have generally declined. Habitat restoration evaluation efforts are critical to ensure efficient use of money and resources but require long-term monitoring of population metrics. Detailed viable salmonid population and life-history data, such as that provided by PIT-tagging and instream PTIS networks inform fisheries policy and management and enable assessment of long-term effects of habitat restoration actions such as the removal of Hemlock Dam on Trout Creek and proposed major instream habitat restoration in the upper Wind River.

Washington↗

USGS2019

Distribution and movement of steelhead and anglers in the Clearwater River, Idaho

Steelhead Oncorhynchus mykiss is a species that is of high economic value that supports popular sport fisheries across the Pacific Northwest. The Clearwater River in Idaho provides a trophy steelhead fishery, and it is home to both wild- and hatchery-origin steelhead. To manage the fishery effectively, information is needed about the spatial and temporal overlap of wild and hatchery steelhead in the Clearwater River, as well as the activity of anglers. We conducted a radiotelemetry study to describe the distribution of steelhead and their final fate in the Clearwater River, and creel surveys were used to describe the distribution of anglers. In total, 289 wild (Potlatch River and Lochsa River) and hatchery (from Dworshak National Fish Hatchery and South Fork Clearwater River) steelhead were radio-tagged at Lower Granite Dam, 51 river kilometers (rkm) downstream from the mouth of the Clearwater River. Fish were monitored upon their entry into the Clearwater River by using mobile tracking surveys (boat and vehicle) and stationary antennas. The majority of wild and hatchery steelhead arrived in the Clearwater River in the fall with the exception of those from the Lochsa River, which arrived in the fall and following spring. Average daily movement of the fish was minimal (range = 0.3–4.7 km/d) and dependent on water temperature and flow. The fates of wild and hatchery steelhead varied. Fish returned to spawning grounds, were harvested by anglers (hatchery fish only), or had unknown fates. Both wild and hatchery steelhead returned at high rates to their natal tributaries and release locations. No straying was observed in either group; however, occasions when steelhead have overshot their natal tributaries and release locations were documented. Spatial and temporal overlap of the distributions of wild and hatchery steelhead was minimal. The distribution of anglers overlapped with that of hatchery steelhead in the fall, winter, and spring. The distributional overlap of anglers and wild steelhead was minimal and largely occurred in September in the lower Clearwater River. This suggests that the Clearwater River has a highly compartmentalized fishery and that current fishing regulations in the Clearwater River are providing for a diversity of angling opportunities while conserving wild steelhead and offering harvest of hatchery fish. The results from this study have important implications for the conservation and management of wild and hatchery steelhead.

Idaho↗

USGS2024

Use of otolith microchemistry to determine natal origin for Silver Carp Hypophthalmichthys molitrix in the lower Mississippi River basin

Silver Carp ( Hypophthalmichthys molitrix ) populations have established and expanded throughout the lower Mississippi River basin (LMRB). Information pertaining to Silver Carp population mixing among rivers within the LMRB is lacking. Documented relations between Silver Carp otolith and river water barium (Ba) and strontium (Sr) microchemical signatures may enable estimation of origins of Silver Carp in the LMRB. Replicate water samples and otoliths from 308 Silver Carp were collected from the Cache, Arkansas, White, Yazoo, St. Francis, L’Anguille, and Mississippi rivers, and Merrisach Lake (situated along a canal connecting the lower reaches of the Arkansas and White rivers) within the LMRB. Water and carp otolith microchemical signatures exhibited consistent differences among water bodies. A classification and regression tree model exhibited 80% accuracy when assigning carp collected from the White, Arkansas, and Mississippi rivers based on fish-water microchemical signatures. Model accuracy decreased as smaller rivers were incorporated into models. Predicted natal origin based on otolith microchemical signatures suggested the White River (43%) and the lower Mississippi River (39%) were the likely origins for ~ 82% of the Silver Carp sampled. Despite the prevalence of adult Silver Carp within the Arkansas River system, fewer (18%) appeared to have originated there compared to the White and Mississippi rivers. Long-term water sampling and additional isotopic measurements may refine analyses to better determine the relative contributions of Silver Carp from the smaller river systems. Population mixing of Silver Carp among tributary rivers appears to be common within the LMRB, and removal efforts may benefit from evaluating the magnitude of fish movement and connectivity among rivers.

lower Mississippi River basin↗

USGS2008

Sources and fate of nitrate in the Illinois River Basin, Illinois

We conducted a two-year investigation into the sources and fate of nitrate (NO3-) in the Illinois River from the Chicago area to the river's confluence with the Mississippi River. Samples from waterways in the Chicago area (Des Plaines River and the Sanitary and Ship Canal) had relatively high concentrations of nitrogen (N) species and NO3- isotopic compositions indicative of treated wastewater (TWW). Downstream of the Brandon Road Lock and Dam, NO3- in tributaries discharging to the Illinois River primarily comes from tiles draining row crops. Nitrate isotopic signatures from these tributaries as well as drain tiles were indicative of synthetic fertilizer and/or soil organic matter (SOM) at various stages of denitrification. Nitrate-N concentrations generally decreased in the Illinois River with distance from the Chicago area primarily due to dilution. The decrease in NO3-N concentrations was especially conspicuous during the summer, when there is minimal discharge from drain tiles and NO3-N concentrations in the tributaries were low. In August 2005, when conditions were very dry, NO3-N concentrations decreased from 7.4 mg/L in the Chicago area to less than 1 mg/L near where the Illinois River discharges to the Mississippi River. The isotopic composition of NO3- in water samples from the Illinois River were a mixture of three end members: (1) fertilizer and/or SOM in drain tile water, typically showing the least amount of denitrification, (2) fertilizer and/or SOM in deeper ground water, showing the highest degree of denitrification, and (3) TWW. There was seasonal variability, depending on the volume of water flowing in the Illinois River. During high flow periods, river water samples plotted closest to those of tile drain samples; during low flow periods, a greater influence of TWW was observed in the isotopic composition. A subset of summer samples from the Chicago waterways had isotopic values plotting near and within the domain that characterizes manure and sewage. Nitrate in the Chicago area is primarily derived from TWW, with its isotopic signature evident downstream at least as far as Pekin during most of the year and all the way to the Mississippi River during periods of low flow. Denitrification occurs predominantly in groundwater between and away from drain tiles, although there is evidence that in-stream denitrification and/or biological uptake of NO3- occurs in the Peoria Lake reach of the Illinois River, at least during periods of low flow in the summer. We calculated that the river was losing about half of its NO3-N load in Peoria Lake in August 2005 (a period of very low flow), at a rate of about 7500 kg/day.

Journal of Hydrology↗

USGS2003

Flood plain and channel dynamics of the Quinault and Queets Rivers, Washington, USA

Comparison of historic channel migration rates, modern planform conditions, and overall sediment, wood, and flow conditions and interactions for the Quinault River and Queets River in the western Olympic Peninsula, Washington, reveals decadal- to century-scale interactions between gravel-bed channels and forested flood plains in temperate maritime environments. The downstream alluvial portions of these two rivers can be divided into three reaches of different slope, flow, sediment, and wood regimes: (i) the upper Quinault River is aggrading behind Lake Quinault, a natural lake that traps most sediment and wood transported from the Olympic Mountain headwaters. (ii) The lower Quinault River, downstream of Lake Quinault, transports only sediment and wood derived from reworking of flood-plain deposits and contributed from valley margins. (iii) The Queets River has unimpeded movement of sediment and water from the mountainous headwaters to the Pacific Ocean. Measurements of channel planform characteristics and historic migration rates and patterns show that these three reaches have correspondingly distinct channel and flood-plain morphologies and dynamics. The aggrading and sediment-rich upper Quinault River has the widest flood plain, widest active channel, greatest number of low-flow channels and flanking gravel bars, and an average channel migration rate of 12.7±3.3 m/year between 1900 and 1994. The comparatively sediment-poor lower Quinault River has the narrowest flood plain, narrowest active channel, and lowest channel migration rate (4.0±1.2 m/year); and most flow is through a single channel with few adjacent gravel bars. The Queets River has attributes intermediate between the lower and upper Quinault Rivers, including an average channel migration rate of 7.5±2.9 m/year. Flood-plain turnover rates are similar for all three reaches, with channels eroding the flood plain at the rate of about 0.2% of the flood-plain area per year, and with corresponding flood-plain half-lives of 300 to 500 years. Observations from this study and previous studies on the Queets River show that channel and flood-plain dynamics and morphology are affected by interactions between flow, sediment, and standing and entrained wood, some of which likely involve time frames similar to 200–500-year flood-plain half-lives. On the upper Quinault River and Queets River, log jams promote bar growth and consequent channel shifting, short-distance avulsions, and meander cutoffs, resulting in mobile and wide active channels. On the lower Quinault River, large portions of the channel are stable and flow within vegetated flood plains. However, locally, channel-spanning log jams have caused channel avulsions within reaches that have been subsequently mobile for several decades. In all three reaches, log jams appear to be areas of conifer germination and growth that may later further influence channel and flood-plain conditions on long time scales by forming flood-plain areas resistant to channel migration and by providing key members of future log jams. Appreciation of these processes and dynamics and associated temporal and spatial scales is necessary to formulate effective long-term approaches to managing fluvial ecosystems in forested environments.

Geomorphology↗

USGS2019

Birth and evolution of the Virgin River fluvial system: ∼1 km of post–5 Ma uplift of the western Colorado Plateau

The uplift history of the Colorado Plateau has been debated for over a century with still no unified hypotheses for the cause, timing, and rate of uplift. 40 Ar/ 39 Ar and K/Ar dating of recurrent basaltic volcanism over the past ∼6 Ma within the Virgin River drainage system, southwest Utah, northwest Arizona, and southern Nevada, provides a way to reconstruct paleoprofiles and quantify differential river incision across the boundary faults of the Colorado Plateau–Basin and Range boundary. We compare differential incision data with patterns of channel steepness, bedrock erodibility, basaltic migration, and mantle velocity structure to understand the birth and evolution of the Virgin River system. New detrital sanidine ages constrain the arrival of the Virgin River across the Virgin Mountains to less than 5.9 Ma. Virgin River incision rates and amounts show an eastward stair-step increase in bedrock incision across multiple N-S–trending normal faults. Using block incision values away from fault-related flexures, average bedrock incision rates are near zero since 4.6 Ma in the Lower Colorado River corridor, 23 m/Ma from 6.8 to 3.6 Ma in the Lake Mead block, 85 m/Ma from 3 to 0.4 Ma in the combined St. George and Hurricane blocks, and 338 m/Ma from 1 to 0.1 Ma in the Zion block. Steady incision within each block is documented by incision constraints that span these age ranges. We test two end-member hypotheses to explain the observed differential incision magnitudes and rates along the Virgin River system over the past ∼5 Ma: (1) as a measure of mantle-driven differential uplift of the Colorado Plateau relative to sea level; or (2) due to river integration across previously uplifted topography and differential rock types with down-dropping of Transition Zone blocks but no post–5 Ma uplift. We favor headwater uplift of the Colorado Plateau because basalt-preserved paleoprofiles indicate that eastern fault blocks have been the “active” blocks that moved upwards relative to western blocks with little base-level change of the lower Colorado River corridor in the past 4.6 Ma. Block-to-block differential incision adds cumulatively such that the Zion block (Colorado Plateau edge) has been deeply incised 880–1200 m (∼338 m/Ma) over the 2.6–3.6 Ma period of Hurricane fault neotectonic movement, which has a slip magnitude of 1100 m. Mantle-driven uplift is implicated by a strong correlation throughout the Virgin River drainage between high normalized channel steepness (k sn ) and low underlying mantle velocity, whereas there is a weaker correlation between high k sn and resistant lithologies. Basaltic volcanism has migrated northeastward at a rate of ∼18 km/Ma parallel to the Virgin River between ca. 13 and 0.5 Ma, also suggesting a mantle-driven mechanism for the combined epeirogenic uplift of the western Colorado Plateau, recurrent slip on its bounding faults, and headward propagation and differential incision of the Virgin River. Thus, we interpret the Virgin River to be a <5 Ma disequilibrium river system responding to ongoing upper-mantle modification and related basalt extraction that has driven ∼1 km of young (and ongoing) surface uplift of the western Colorado Plateau.

Arizona, Nevada, Utah↗

USGS2016

Distributions of small nongame fishes in the lower Yellowstone River

The Yellowstone River is the longest unimpounded river in the conterminous United States. It has a relatively natural flow regime, which helps maintain diverse habitats and fish assemblages uncommon in large rivers elsewhere. The lower Yellowstone River was thought to support a diverse nongame fish assemblage including several species of special concern. However, comprehensive data on the small nongame fish assemblage of the lower Yellowstone River is lacking. Therefore, we sampled the Yellowstone River downstream of its confluence with the Clark’s Fork using fyke nets and otter trawls to assess distributions and abundances of small nongame fishes. We captured 42 species (24 native and 18 nonnative) in the lower Yellowstone River with fyke nets. Native species constituted over 99% of the catch. Emerald shiners Notropis atherinoides , western silvery minnows Hybognathus argyritis , flathead chubs Platygobio gracilis , sand shiners Notropis stramineus , and longnose dace Rhinichthys cataractae composed nearly 94% of fyke net catch and were caught in every segment of the study area. We captured 24 species by otter trawling downstream of the Tongue River. Sturgeon chubs Macrhybopsis gelida , channel catfish Ictalurus punctatus , flathead chubs, stonecats Noturus flavus , and sicklefin chubs Macrhybopsis meeki composed 89% of the otter trawl catch. The upstream distributional limit of sturgeon chubs in the Yellowstone River was the Tongue River; few sicklefin chubs were captured above Intake Diversion Dam. This study not only provides biologists with baseline data for future monitoring efforts on the Yellowstone River but serves as a benchmark for management and conservation efforts in large rivers elsewhere as the Yellowstone River represents one of the best references for a naturally functioning Great Plains river.

Montana↗

USGS1996

Gold placers of the historical Fortymile River region, Alaska

The Fortymile River region in east-central Alaska has a long and colorful history as the site of the first major gold discovery in interior Alaska. Placer gold has been mined in the region nearly every year since its original discovery in 1886. Total gold production is approximately 500,000 troy ounces. Although many of the rich deposits have been mined, there still exist areas that contain gold. Areas of mined and unmined gold-bearing creek and terrace gravels are outlined on the accompanying geologic map. The early history of the Fortymile area centered on the small frontier settlement of Fortymile City located at the junction of the Fortymile and Yukon Rivers in Canadian territory. This was the supply and jumping-off point for prospectors who worked their way into Alaska up the Fortymile River and found gold on many of its tributaries. Hand mining, both underground and surface, using sluice boxes and (or) rockers were the earliest methods; later, hydraulicking, dredging, and draglining methods were used. More recently, bulldozers and elevated trammels have been used, as well as very portable floating suction dredges. The rich mining lore of the area is closely associated with events of the nearby world-famous Klondike District. Bedrock and placer geology and mining history of individual gold-rich creeks are herein updated. The Fortymile area, which is part of the Yukon-Tanana Upland, contains quartzite, schist, gneiss, amphibolite, marble, serpentinite, and granite overlain by basalt, sandstone, conglomerate, shale, tuff, and coal; overlying these rocks are several deposits of varying ages consisting of gold-bearing gravel and colluvium. The close spatial association of creeks containing placer gold and the gneiss, schist, amphibolite, and marble unit strongly suggests this metamorphic unit is the gold source. High terrace gravels record a time from the late Tertiary to early Pleistocene when the ancestral Fortymile River and its major tributaries, the North and South Forks, had floodplains roughly 1 to 2 miles (2-3 kilometers) wide and gradients of about 4 feet per mile (0.75 meters per kilometer). Base-level lowering during the post-early Pleistocene caused the rivers to cut into their floodplains and to develop the youthful characteristics they have today such as V-shaped canyons, narrow floodplains, and gradients of at least twice those of the old river. Colluvium marginal to creek deposits in steep-sided valleys is often gold bearing. Much of the unconsolidated gravel within the major drainages of the Fortymile River, South Fork, North Fork, and Mosquito Fork is colluvium. Heavy-mineral-concentrate samples from the gold-producing creeks and high terrace gravels contain varying amounts of magnetite (20 to 80 percent) and ilmenite (10 to 30 percent), and samples from creeks draining areas principally composed of metamorphic rocks contain abundant garnet (10 to 30 percent). Gold fineness ranges from 620 to 927, but it is difficult to attach any geologic significance to the fineness data. Most placer gold in the Fortymile River area has been recovered at, or near, the gravelbedrock contact. The lowermost 3.3 feet (1 meter) of gravel and the uppermost 1.6 feet (0.5 meter) of bedrock may contain as much as 80 to 90 percent of the gold that is ultimately recovered. Gold nuggets are rare and most of the gold recovered is in the form of flattened fragments less than .2 inches (5 millimeters) in greatest dimension. However, large gold nuggets have been found on Wade Creek; examples are ones of 25,33,56, and 70 ounces. Occasionally, large nuggets may still be found in the tailing piles along the creek. The Fortymile River and its tributaries the South Fork, Walker Fork, and Mosquito Fork, all of which at one time were the sites of bucket-line dredge operations, now are almost exclusively mined using floating suction dredges. Unmined gold-bearing gravel is present in the floodplain of the Walker Fork valley below Cherry Creek and in low (about 100 to 130 feet or 30 to 40 meters) terraces along the north side of Walker Fork and east side of Cherry Creek. Considering the locations of where most gold has been found in the South Fork valley both by the older bucket dredges and the modern suction dredges, it seems likely that the tributary drainages of Lost Chicken, Napoleon, Franklin, and Buckskin Creeks have supplied the bulk of the gold to the South Fork valley. A quarter acre (0.10 hectare), 130-foot-thick ( 40 meters) section of the high terrace gravels on the north side of Napoleon Creek was mined for placer gold and yielded values estimated to be $8.50 per cubic yard (or $6.50 per cubic meter) at $350 per troy ounce. The unmined high terrace gravels on the south side of Buckskin Creek contain gold; however, this gravel is only 3 to 6.5 feet (1 to 2 meters) thick. The search for a lode gold source in the Fortymile River region may be in vain, because substantially more gold than has been recovered from the placers can be derived by the gradual erosion of large volumes of source rocks that contain background mean gold amounts. Using Leon's mass balance equation, 5,167 metric tons of gold may exist in the placers of the Fortymile River region, less than 1 percent of the recovered amount of 15.6 tons. The largest gold resource remaining in the Fortymile River region is probably in the high terrace gravels exposed along many of the creeks and rivers. Until there is exploratory drilling or a comprehensive sampling program, the amount of gold in these gravels will remain unknown. Environmental constraints imposed by Federal and State agencies have slowed, but not stopped, placer mining in the Fortymile River area, and a significant gold price rise would result in more mining.

Alaska↗

USGS1952

Hydrologic reconnaissance of the Green River in Utah and Colorado

The Green River, rising in Wyoming and draining high mountains in that state, northeast Utah and northwest Colorado, is a major tributary of the Colorado River. In the late summer, after the snow has melted from these mountains, the flow in the Green River reaches its minimum for the year. At that time a large proportion of the water in the river is returned to the atmosphere by evaporation and transpiration. During a 21-day period in September 1948, when the flow was least for the year, the average flow of the river as it entered Utah from Wyoming was 515 cfs. In the 437 miles of its course through Utah and Colorado evapotranspiration losses averaged 430 cfs. The average discharge of the Green River into the Colorado was about 975 cfs. Contributions to the river in Utah and Colorado totalled 890 cfsi including 560 from tributaries. The calculated ground-water inflow was about 330 cfs, of which about 75 percent was contributed within the Uinta Basin. Verv little ground water was contributed to the river in the lower 180 miles of its course, where the river flows through canyon lands of the Colorado Plateaus. These estimates are based upon information collected during a boat reconnaissance in September 1948, and upon data available from stream-gaging stations along the Green River and many of its tributaries. From these data an accounting was made of the water--as to both quantity and quality--in several segments of the river. For each segment determinations were made of the surface outflow, loss by evapotranspiration, and surface- and ground-water inflow. During the reconnaissance information was also obtained as to the relation of stream flow to regional geology and ground-water hydrology. No detailed hydrologic studies have yet been made within the drainage basin of the Green River. On the basis of this recomiaissance, detailed studies in the Uinta Basin, Browns Park, and Echo Park areas are recommended as highly desirable, because of the possible relations of ground-water hydrology to river-basin development projects. Similar reconnaissance can be of value in delineating the areas where detailed hydrologic studies would be most fruitful throughout the upper Colorado River basin.

Colorado, Utah↗

USGS2003

Regional sediment budget of the Columbia River littoral cell, USA: Analysis of bathymetric- and topographic-volume change

In this Open-File Report we present calculations of changes in bathymetric and topographic volumes for the Grays Harbor, Willapa Bay, and Columbia River entrances and the adjacent coasts of North Beach, Grayland Plains, Long Beach, and Clatsop Plains for four intervals: pre-jetty - 1920s (Interval 1), 1920s - 1950s (Interval 2), 1950s - 1990s (Interval 3), and 1920s 1990s (Interval 4). This analysis is part of the Southwest Washington Coastal Erosion Study (SWCES), the goals of which are to understand and predict the morphologic behavior of the Columbia River littoral cell on a management scale of tens of kilometers and decades. We obtain topographic Light Detection and Ranging (LIDAR) data from a joint project by the U.S. Geological Survey (USGS), National Oceanic and Atmospheric Administration (NOAA), National Aeronautic and Space Administration (NASA), and the Washington State Department of Ecology (DOE) and bathymetric data from the U.S. Coast and Geodetic Survey (USC&GS), U.S. Army Corps of Engineers (USACE), USGS, and the DOE. Shoreline data are digitized from T-Sheets and aerial photographs from the USC&GS and National Ocean Service (NOS). Instead of uncritically adjusting each survey to NAVD88, a common vertical land-based datum, we adjust some surveys to produce optimal results according to the following criteria. First, we minimize offsets in overlapping surveys within the same era, and second, we minimize bathymetric changes (relative to the 1990s) in deep water, where we assume minimal change has taken place. We grid bathymetric and topographic datasets using kriging and triangulation algorithms, calculate bathymetric-change surfaces for each interval, and calculate volume changes within polygons that are overlaid on the bathymetric-change surfaces. We find similar morphologic changes near the entrances to Grays Harbor and the Columbia River following jetty construction between 1898 and 1916 at the Grays Harbor entrance and between 1885 and 1913 at the Columbia River entrance. The inlets and inner deltas eroded and the outer deltas moved offshore and accreted. The adjacent coasts experienced accretion over alongshore distances of tens of kilometers. North of the Grays Harbor entrance along North Beach and north of the Columbia River entrance along Long Beach the shoreface and the beach-dune complex mainly prograded, whereas south of the Grays Harbor entrance along Grayland Plains and south of the Columbia River entrance along Clatsop Plains the beach-dune complex above -10 m NAVD88 prograded and the shoreface between approximately -30 m and -10 m NAVD88 eroded. In the decades following jetty construction, the rates of erosion and accretion at the entrances decreased and the centers of deposition along the adjacent coasts moved away from the entrances. The rates of change have decreased, suggesting the systems are approaching dynamic equilibrium. Exceptions to this behaviour are the accretion of the beach-dune complex of Long Beach, the erosion of Cape Shoalwater, and the northward migration of the Willapa Bay ebb-tidal delta during all intervals. The net shoreline advance of Long Beach increases from 0.28 m/yr in pre-jetty conditions to 3.78 m/yr during Interval 4. The erosion of Cape Shoalwater and the northward migration of the Willapa Bay ebb-tidal delta are related to the northern migration of the Willapa Bay North Channel. Volume changes at the Grays Harbor, Willapa Bay, and Columbia River entrances and the Columbia River estuary are balanced against losses and gains due to littoral transport and sand supply from the Columbia River. Based on these sediment balances, we infer the following pathways: sand that eroded from the inlets and inner deltas at the Grays Harbor and Columbia River entrances moved offshore and northward to accrete the outer deltas and the beaches to the north; sand from the south flank of the Grays Harbor delta and shelf along Grayland Plains moved onshore to accrete the beach dune complex of Grayland Plains and moved northward to maintain accretion of the outer delta and the beach-dune complex of North Beach; sand that eroded from the south flank of the Columbia River delta and shelf along Clatsop Plains contributed to the accretion of the beach-dune complex of Clatsop Plains and the Columbia River outer delta. The net volume change for Interval 1 and 3 at the Grays Harbor entrance and for Interval 1 at the Columbia River entrance is erosion, whereas the net change for the other intervals is accretion. For the entire CRLC, there is a net loss of 185 Mm 3 for Interval 1, a net gain of 357 Mm 3 for Interval 2, and a net gain of 187 Mm 3 for Interval 3. These imbalances can be the result of incomplete bathymetric coverage of the bays and shoreface, uncertainties in the adjustments of vertical tidal datums, inconsistencies in the bathymetric data, and uncertainties in the sediment supply of the Columbia River.

Oregon, Washington↗

USGS2009

Summary of Migration and Survival Data from Radio-Tagged Juvenile Coho Salmon in the Trinity River, Northern California, 2008

The survival of hatchery-origin juvenile coho salmon from the Trinity River Hatchery was estimated as they migrated seaward through the Trinity and Klamath Rivers. The purpose of the study was to collect data for comparison to a similar study in the Klamath River and provide data to the Trinity River Restoration Program. A total of 200 fish fitted with radio transmitters were released into the Trinity River near the hatchery (river kilometer 252 from the mouth of the Klamath River) biweekly from March 19 to May 28, 2008. Fish from the earliest release groups took longer to pass the first detection site 10 kilometers downstream of the hatchery than fish from the later release groups, but travel times between subsequent sites were often similar among the release groups. The travel times of individuals through the 239 kilometer study area ranged from 15.5 to 84.6 days with a median of 43.3 days. The data and models did not support differences in survival among release groups, but did support differences among river reaches. The probability of survival in the first 53 kilometers was lower than in the reaches farther downstream, which is similar to trends in juvenile coho salmon in the Klamath River. The lowest estimated survival in this study was in the first 10 kilometers from release in the Trinity River (0.676 SE 0.036) and the highest estimated survival was in the final 20 kilometer reach in the Klamath River (0.987 SE 0.013). Estimated survivals of radio-tagged juvenile coho salmon from release to Klamath River kilometer 33 were 0.639 per 100 kilometers for Trinity River fish and 0.721 per 100 kilometers for Klamath River fish.

Open-File Report↗

USGS2011

Movement of bull trout in the upper Jarbidge River watershed, Idaho and Nevada, 2008-09--A supplement to Open-File Report 2010-1033

We monitored bull trout ( Salvelinus confluentus ) in 2008 and 2009 as a continuation of our work in 2006 and 2007, which involved the tagging of 1,536 bull trout with passive integrated transponder (PIT) tags in the East Fork Jarbidge River and West Fork Jarbidge River and their tributaries in northeastern Nevada and southern Idaho. We installed PIT tag interrogation systems (PTISs) at established locations soon after ice-out, and maintained the PTISs in order to collect information on bull trout movements through December of each year. We observed a marked increase of movement in 2008 and 2009. Bull trout tagged in the uppermost portions of the East Fork Jarbidge River at altitudes greater than 2,100 meters moved to the confluence of the East Fork Jarbidge River and West Fork Jarbidge River in summer and autumn. Ten bull trout tagged upstream of the confluence of Pine Creek and the West Fork Jarbidge River moved downstream and then upstream in the East Fork Jarbidge River, and then past the PTIS at Murphy Hot Springs (river kilometer [rkm] 4.1). Two of these fish ascended Dave Creek, a tributary of the East Fork Jarbidge River, past the PTIS at rkm 0.4. One bull trout that was tagged at rkm 11 in Dave Creek on June 28, 2007 moved downstream to the confluence of the East Fork Jarbidge River and West Fork Jarbidge River (rkm 0) on July 28, 2007, and it was then detected in the West Fork Jarbidge River moving past our PTIS at rkm 15 on May 4, 2008. Combined, the extent and types of bull trout movements observed indicated that the primarily age-1 and age-2 bull trout that we tagged in 2006 and 2007 showed increased movement with age and evidence of a substantial amount of fluvial life history. The movements suggest strong connectivity between spawning areas and downstream mainstem areas, as well as between the East Fork Jarbidge River and West Fork Jarbidge River.

Open-File Report↗

USGS2013

Streamflow characterization and summary of water-quality data collection during the Mississippi River flood, April through July 2011

From April through July 2011, the U.S. Geological Survey collected surface-water samples from 69 water-quality stations and 3 flood-control structures in 4 major subbasins of the Mississippi River Basin to characterize the water quality during the 2011 Mississippi River flood. Most stations were sampled at least monthly for field parameters suspended sediment, nutrients, and selected pesticides. Samples were collected at daily to biweekly frequencies at selected sites in the case of suspended sediment. Hydro-carbon analysis was performed on samples collected at two sites in the Atchafalaya River Basin to assess the water-quality implications of opening the Morganza Floodway. Water-quality samples obtained during the flood period were collected at flows well above normal streamflow conditions at the majority of the stations throughout the Mississippi River Basin and its subbasins. Heavy rainfall and snowmelt resulted in high streamflow in the Mississippi River Basin from April through July 2011. The Ohio River Subbasin contributed to most of the flow in the lower Mississippi-Atchafalaya River Subbasin during the months of April and May because of widespread rainfall, whereas snowmelt and precipitation from the Missouri River Subbasin and the upper Mississippi River Subbasin contributed to most of the flow in the lower Mississippi-Atchafalaya River Subbasin during June and July. Peak streamflows from the 2011 flood were higher than peak streamflow during previous historic floods at most the selected streamgages in the Mississippi River Basin. In the Missouri River Subbasin, the volume of water moved during the 1952 flood was greater than the amount move during the 2011 flood. Median concentrations of suspended sediment and total phosphorus were higher in the Missouri River Subbasin during the flood when compared to the other three subbasins. Surface water in the upper Mississippi River Subbasin contained higher median concentrations of total nitrogen, nitrate, orthophosphate, and atrazine during the flood period.

Mississippi River Basin↗

USGS2014

Demographics and run timing of adult Lost River ( Deltistes luxatus ) and short nose ( Chasmistes brevirostris ) suckers in Upper Klamath Lake, Oregon, 2012

Data from a long-term capture-recapture program were used to assess the status and dynamics of populations of two long-lived, federally endangered catostomids in Upper Klamath Lake, Oregon. Lost River suckers ( Deltistes luxatus ) and shortnose suckers ( Chasmistes brevirostris ) have been captured and tagged with passive integrated transponder (PIT) tags during their spawning migrations in each year since 1995. In addition, beginning in 2005, individuals that had been previously PIT-tagged were re-encountered on remote underwater antennas deployed throughout sucker spawning areas. Captures and remote encounters during spring 2012 were used to describe the spawning migrations in that year and also were incorporated into capture-recapture analyses of population dynamics. Cormack-Jolly-Seber (CJS) open population capture-recapture models were used to estimate annual survival probabilities, and a reverse-time analog of the CJS model was used to estimate recruitment of new individuals into the spawning populations. In addition, data on the size composition of captured fish were examined to provide corroborating evidence of recruitment. Model estimates of survival and recruitment were used to derive estimates of changes in population size over time and to determine the status of the populations in 2011. Separate analyses were conducted for each species and also for each subpopulation of Lost River suckers (LRS). Shortnose suckers (SNS) and one subpopulation of LRS migrate into tributary rivers to spawn, whereas the other LRS subpopulation spawns at groundwater upwelling areas along the eastern shoreline of the lake. In 2012, we captured, tagged, and released 749 LRS at four lakeshore spawning areas and recaptured an additional 969 individuals that had been tagged in previous years. Across all four areas, the remote antennas detected 6,578 individual LRS during the spawning season. Spawning activity peaked in April and most individuals were encountered at Cinder Flats and Sucker Springs. In the Williamson River, we captured, tagged, and released 3,376 LRS and 299 SNS, and recaptured 551 LRS and 125 SNS that had been tagged in previous years. Remote PIT tag antennas in the traps at the weir on the Williamson River and remote antenna systems that spanned the river at four different locations on the Williamson and Sprague Rivers detected a total of 19,321 LRS and 6,124 SNS. Most LRS passed upstream between late April and mid-May when water temperatures were increasing and greater than 10 °C. In contrast, most upstream passage for SNS occurred in early and mid-May when water temperatures were increasing and near or greater than 12 °C. Finally, an additional 1,188 LRS and 1,665 SNS were captured in trammel net sampling at pre-spawn staging areas in the northeastern part of the lake. Of these, 291 of the LRS and 653 of the SNS had been PIT-tagged in previous years. For LRS captured at the staging areas that had encounter histories that were informative about their spawning location, over 90 percent of the fish were members of the subpopulation that spawns in the rivers. Capture-recapture analyses for the LRS subpopulation that spawns at the shoreline areas included encounter histories for more than 12,150 individuals, and analyses for the subpopulation that spawns in the rivers included more than 29,500 encounter histories. With a few exceptions, the survival of males and females in both subpopulations was high (greater than 0.9) between 1999 and 2010. Notably lower survival occurred for both sexes from the rivers in 2000, for both sexes from the shoreline areas in 2002, and for males from the rivers in 2006. Between 2001 and 2011, the abundance of males in the lakeshore spawning subpopulation decreased by 53–65 percent and the abundance of females decreased by 36–48 percent. Capture-recapture models suggested that the abundance of both sexes in the river spawning subpopulation of LRS had increased substantially since 2006; increases were due to large estimated recruitment events in 2006 and 2008. We know that the estimates in 2006 are substantially biased in favor of recruitment because of a sampling issue. We are skeptical of the magnitude of recruitment indicated by the 2008 estimates as well because (1) few small individuals that would indicate the presence of new recruits were captured in that year, and (2) recapture probabilities in recruitment models based on just physical recaptures were lower than desired for robust inferences from capture-recapture models. If we assume that little or no recruitment occurred in 2006 or 2008, the abundance of both sexes in the river spawning subpopulation likely has decreased at rates similar to the rates for the lakeshore spawning subpopulation between 2002 and 2011. Capture-recapture analyses for SNS included encounter histories for more than 17,700 individuals. Most annual survival estimates between 2001 and 2010 were high (greater than 0.8), but SNS experienced more years of low survival than either LRS subpopulation. Annual survival of both sexes was particularly low in 2001, 2004, and 2010. In addition, male survival was somewhat low in 2002. Capture-recapture models and size composition data indicate that recruitment of new individuals into the SNS spawning population was trivial between 2001 and 2005. Models indicate substantial recruitment of new individuals into the SNS spawning population in 2006, 2008, and 2009. As a result, capture-recapture modeling suggests that the abundance of adult spawning SNS was relatively stable between 2006 and 2010. We are skeptical of the estimated recruitment in 2006, 2008, and 2009 because few small individuals that would indicate the presence of new recruits were captured in any of those years, and recapture probabilities in recruitment models were low. The best-case scenario for SNS, based on capture-recapture recruitment modeling, indicates that the abundance of males in the spawning population decreased by 71 percent and the abundance of females decreased by 69 percent between 2001 and 2011. The worst-case scenario, which assumes no recruitment and seems more likely, suggests an 86 percent decrease for males and an 81 percent decrease for females. Despite relatively high survival in most years, we conclude that both species have experienced substantial declines in the abundance of spawning fish because losses from mortality have not been balanced by recruitment of new individuals. Although capture-recapture data indicate substantial recruitment of new individuals into the adult spawning populations for SNS and river spawning LRS in some years, size data do not corroborate these estimates. In fact, fork length data indicate that all populations are largely comprised of fish that were present in the late 1990s and early 2000s. As a result, the status of the endangered sucker populations in Upper Klamath Lake remains worrisome, and the situation is especially dire for shortnose suckers. Future investigations should explore the connections between sucker recruitment and survival and various environmental factors, such as water quality and disease. Our monitoring program provides a robust platform for estimating vital population parameters, evaluating the status of the populations, and assessing the effectiveness of conservation and recovery efforts.

Oregon↗

USGS2015

Status and trends of adult Lost River ( Deltistes luxatus ) and shortnose ( Chasmistes brevirostris ) sucker populations in Upper Klamath Lake, Oregon, 2014

Executive Summary Data from a long-term capture-recapture program were used to assess the status and dynamics of populations of two long-lived, federally endangered catostomids in Upper Klamath Lake, Oregon. Lost River suckers ( Deltistes luxatus ) and shortnose suckers ( Chasmistes brevirostris ) have been captured and tagged with passive integrated transponder (PIT) tags during their spawning migrations in each year since 1995. In addition, beginning in 2005, individuals that had been previously PIT-tagged were re-encountered on remote underwater antennas deployed throughout sucker spawning areas. Captures and remote encounters during the spawning season in spring 2014 were incorporated into capture-recapture analyses of population dynamics. Cormack-Jolly-Seber (CJS) open population capture-recapture models were used to estimate annual survival probabilities, and a reverse-time analog of the CJS model was used to estimate recruitment of new individuals into the spawning populations. In addition, data on the size composition of captured fish were examined to provide corroborating evidence of recruitment. Model estimates of survival and recruitment were used to derive estimates of changes in population size over time and to determine the status of the populations through 2013. Separate analyses were conducted for each species and also for each subpopulation of Lost River suckers (LRS). Shortnose suckers (SNS) and one subpopulation of LRS migrate into tributary rivers to spawn, whereas the other LRS subpopulation spawns at groundwater upwelling areas along the eastern shoreline of the lake. In 2014, we captured, tagged, and released 496 LRS at four lakeshore spawning areas and recaptured an additional 970 individuals that had been tagged in previous years. Across all four areas, the remote antennas detected 6,370 individual LRS during the spawning season. Spawning activity peaked in April and most individuals were encountered at Cinder Flats and Sucker Springs. In the Williamson River, we captured, tagged, and released 3,038 LRS and 267 SNS, and recaptured 762 LRS and 156 SNS that had been tagged in previous years. Remote PIT tag antennas in the traps at the weir on the Williamson River and remote antenna systems that spanned the river at three different locations on the Williamson and Sprague Rivers detected a total of 23,446 LRS and 6,259 SNS. Most LRS passed upstream in the first and second weeks of April when water temperatures were increasing and greater than 10 °C. In contrast, upstream passage for SNS occurred in two pulses, one in early April and one in late April to early May, when water temperatures were increasing and near or greater than 12 °C. Finally, an additional 375 LRS and 884 SNS were captured in trammel net sampling at pre-spawn staging areas in the northeastern part of the lake. Of these, 111 of the LRS and 390 of the SNS had been PIT-tagged in previous years. For LRS captured at the staging areas that had encounter histories that were informative about their spawning location, 79 percent of the fish were members of the subpopulation that spawns in the rivers. Capture-recapture analyses for the LRS subpopulation that spawns at the shoreline areas included encounter histories for more than 13,200 individuals, and analyses for the subpopulation that spawns in the rivers included more than 36,400 encounter histories. With a few exceptions, the survival of males and females in both subpopulations was high (greater than 0.88) between 1999 and 2012. Notably lower survival occurred for both sexes from the rivers in 2000, for males from the shoreline areas in 2002, and for males from the rivers in 2006 and 2012. Between 2001 and 2013, the abundance of males in the lakeshore spawning subpopulation decreased by at least 55 percent and the abundance of females decreased by at least 42 percent. Capture-recapture models suggested that the abundance of both sexes in the river spawning subpopulation of LRS had increased substantially since 2006; increases were mostly due to large estimated recruitment events in 2006 and 2008. We know that the estimates in 2006 are substantially biased in favor of recruitment because of a sampling issue. We are skeptical of the magnitude of recruitment indicated by the 2008 estimates as well because (1) few small individuals that would indicate the presence of new recruits were captured in that year, and (2) recapture probabilities in recruitment models based on just physical recaptures of fish were lower than desired for robust inferences from capture-recapture models. If we assume instead that little or no recruitment occurred for this subpopulation, the abundance of both sexes in the river spawning subpopulation likely has decreased at rates similar to the rates for the lakeshore spawning subpopulation between 2002 and 2013. Capture-recapture analyses for SNS included encounter histories for more than 19,200 individuals. Most annual survival estimates between 2001 and 2012 were high (greater than 0.80), but SNS experienced more years of low survival than either LRS subpopulation. Annual survival of both sexes was relatively low in 2004, 2010, and 2012. In addition, male survival was low in 2002. Capture-recapture models and size composition data indicate that recruitment of new individuals into the SNS spawning population was trivial between 2001 and 2005. Models indicate that more than 10 percent of the population was new recruits in a number of more recent years. As a result, capture-recapture modeling suggests that the abundance of adult spawning SNS was relatively stable between 2006 and 2010. We are skeptical of the estimated recruitment in 2006 because of the known sampling issue. We also are skeptical of the estimated recruitment in other recent years because few small individuals that would indicate the presence of new recruits were captured in any of those years, and recapture probabilities in recruitment models were low. The best-case scenario for SNS, based on capture-recapture recruitment modeling, indicates that the abundance of males in the spawning population decreased by 77 percent and the abundance of females decreased by 73 percent between 2001 and 2013. Decreases in abundance for both sexes likely are greater than these estimates indicate. Despite relatively high survival in most years, we conclude that both species have experienced substantial decreases in the abundance of spawning adults because losses from mortality have not been balanced by recruitment of new individuals. Although capture-recapture data indicate substantial recruitment of new individuals into the spawning populations for SNS and river spawning LRS in some years, size data do not corroborate these estimates. As a result, the status of the endangered sucker populations in Upper Klamath Lake remains worrisome, especially for shortnose suckers. Our monitoring program provides a robust platform for estimating vital population parameters, evaluating the status of the populations, and assessing the effectiveness of conservation and recovery efforts.

Oregon↗

USGS2018

Effects of the proposed California WaterFix North Delta Diversion on survival of juvenile Chinook salmon (Oncorhynchus tshawytscha) in the Sacramento-San Joaquin River Delta, northern California

The California Department of Water Resources and Bureau of Reclamation propose new water intake facilities on the Sacramento River in northern California that would convey some of the water for export to areas south of the Sacramento-San Joaquin River Delta (hereinafter referred to as the Delta) through tunnels rather than through the Delta. The collection of water intakes, tunnels, pumping facilities, associated structures, and proposed operations are collectively referred to as California WaterFix. The water intake facilities, hereinafter referred to as the North Delta Diversion (NDD), are proposed to be located on the Sacramento River downstream of the city of Sacramento and upstream of the first major river junction where Sutter Slough branches from the Sacramento River. The NDD can divert a maximum discharge of 9,000 cubic feet per second (ft3 /s) from the Sacramento River, which reduces the amount of Sacramento River inflow into the Delta. In this report, we conduct four analyses to investigate the effect of the NDD and its proposed operation on survival of juvenile Chinook salmon (Oncorhynchus tshawytscha). All analyses used the results of a Bayesian survival model that allowed us to simulate travel time, migration routing, and survival of juvenile Chinook salmon migrating through the Delta in response to NDD operations, which affected both inflows to the Delta and operation of the Delta Cross Channel (DCC). For the first analysis, we evaluated the effect of the NDD bypass rules on salmon survival. The NDD bypass rules are a set of operational rule curves designed to provide adaptive levels of fish protection by defining allowable diversion rates as a function of (1) Sacramento River discharge as measured at Freeport, and (2) time of year when endangered runs requiring the most protection are present. We determined that all bypass rule curves except constant low-level pumping (maximum diversion of 900 ft3 /s) could cause a sizeable decrease in survival by as much as 6–10 percentage points. The maximum decrease in survival occurred at an intermediate Sacramento River flow of about 20,000–30,000 ft3 /s. Diversion rates increased rapidly as Sacramento River flows increased from 20,000 ft3 /s to 30,000 ft3 /s, until a maximum diversion rate was reached at 9,000 ft3 /s. Because through-Delta survival increases sharply over this range of Sacramento River flow before beginning to level off with further flow increases, increasing diversion rates over this flow range causes a large decrease in survival relative to no diversion. For the second analysis, we applied the survival model to 82 years of daily simulated flows under the Proposed Action (PA) and No Action Alternative (NAA). The PA includes operation of the Central Valley Project/State Water Project with implementation of the NDD and its operations prescribed by the NDD bypass rules, whereas the NAA assumes system operations without implementation of the NDD. We also evaluated a “Level 1” (L1) scenario, which was similar to the PA scenario but applied the most protective bypass rule known as Level 1 post-pulse operations. We noted a high probability that survival under the PA scenario was lower than under the NAA scenario, and that travel time was longer under PA relative to NAA in most simulation years. However, the largest survival differences between the PA and NAA scenarios occurred during October–November and May–June. Although bypass rules are less restrictive during these periods, we determined that more frequent use of the DCC under PA led to the largest differences in survival between the two scenarios. Additionally, we noted no difference in median survival decreases between the PA and L1 scenarios, although in some years the L1 scenario had a lower survival decrease than the PA scenario. For the third analysis, we proposed a quantitative approach for developing NDD rule curves (that is, prescribed diversion flows for given inflows) by using the survival model to identify diversion rates that meet a criterion of a having a small probability of exceeding a given decrease in survival. We examined diversion rates that led to a 10% chance of exceeding a given decrease in survival for a range of absolute and relative decreases in survival. To maintain a given constant level of protection across the range of river flows, our analysis indicated that diversions had to increase at a much slower rate with respect to Sacramento River flow relative to the rule curves defined in the NDD bypass table. Additionally, we determined that diversion rates could be higher than under the bypass table rule curves at river flows less than 20,000 ft3 /s, but diversions had to be less than defined by NDD bypass rules at higher flows. For the fourth analysis, we simulated the effect of “real-time operations” on salmon survival, where bypass flow rates were determined by the presence of juvenile salmon entering the Delta, as indicated by juvenile salmon catch in a rotary screw trap upstream of the Delta. For this analysis, we evaluated NDD operations as defined by the L1 scenario and an additional scenario (Unlimited Pulse Protection [UPP]) that provided protection to an unlimited number of fish pulses. This analysis indicated that the highest catches occurred during flow pulses when daily survival was high, which caused annual survival to be weighted towards periods of high daily survival, resulting in a high annual survival. We determined that the mean annual survival decreased by 1–4 percentage points, and annual survival decreases were more frequently smaller for the UPP scenario. Additionally, because the UPP scenario protected an unlimited number of fish pulses, decreases in daily survival under the UPP scenario were less than under the L1 scenario.

California↗

USGS1988

User's guide for RIV2; a package for routing and accounting of river discharge for a modular, three-dimensional, finite-difference, ground- water flow model

RIV2 is a package for the U.S. Geological Survey 's modular, three-dimensional, finite-difference, groundwater flow model developed by M. G. McDonald and A. W. Harbaugh that simulates river-discharge routing. RIV2 replaces RIVI, the original river package used in the model. RIV2 preserves the basic logic of RIV1, but better represents river-discharge routing. The main features of RIV2 are (1) The river system is divided into reaches and simulated river discharge is routed from one node to the next. (2) Inflow (river discharge) entering the upstream end of a reach can be specified. (3) More than one river can be represented at one node and rivers can cross, as when representing a siphon. (4) The quantity of leakage to or from the aquifer at a given node is proportional to the hydraulic-head difference between that specified for the river and that calculated for the aquifer. Also, the quantity of leakage to the aquifer at any node can be limited by the user and, within this limit, the maximum leakage to the aquifer is the discharge available in the river. This feature allows for the simulation of intermittent rivers and drains that have no discharge routed to their upstream reaches. (5) An accounting of river discharge is maintained. Neither stage-discharge relations nor storage in the river or river banks is simulated. (USGS)

Open-File Report↗