Search USGS⌕ Search

SEARCH · Search USGS

Results for “Valley Habitats”

Search indexed USGS publications on groundwater, aquifers, geologic maps, mineral resources and earthquakes. Explore source records by subject and place.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 379 records · Page 21Linked to original sources
USGS2023

Sediment transport in two tributaries to the San Joaquin River immediately below Friant Dam—Cottonwood Creek and Little Dry Creek, California

Two tributaries to the greater San Joaquin River watershed, Cottonwood and Little Dry Creeks, in California’s Central Valley, were assessed for sediment and streamflow dynamics between October 1, 2011, and September 30, 2019. The two systems deliver sediment to the San Joaquin River below Friant Dam, California. Dams create downstream discontinuities in streamflow and sediment transport and therefore influence fish habitat and sediment dynamics. Because these two creeks are directly downriver from Friant Dam, they become the most upstream source of sediment to the San Joaquin River below Friant Dam. The quality and quantity of spawning habitat for fish in the gravel-bedded reach of the San Joaquin River relies on a range of bed material particle size suitable for redd structure. The effects of coarse-sand to fine-gravel supply on salmonid habitat depends primarily on the size of the sediment and the timing of its addition from tributaries to the San Joaquin River; thus, understanding the timing, quantity, and size of sediment supplied from these two tributaries is critical to the management of ecological and biological sustainability. Streamflow from Cottonwood and Little Dry Creeks, along with streamflow from the San Joaquin River below Friant Dam, were compared to continuously measured water-surface elevations to quantify the timing and direction of streamflow. Suspended-sediment samples were collected with multiple automatic samplers and analyzed for concentration and grain-size distribution. Measured suspended-sediment concentrations and streamflows were used to develop sediment rating curves and compute continuous estimates of suspended-sediment load for each tributary. Satellite imagery was used to qualify spatial and temporal dynamics through the lower watersheds and support more quantitative sediment-load estimates. Computed annual sediment loads ranged from 1.32x10 1 to 2.68x10 4 metric tons for Little Dry Creek and 9.82 to 1.98x10 3 metric tons for Cottonwood Creek. Sediment loads computed during the study period for both watersheds show that annual loads were highest during water year 2017 (October 1, 2016, to September 30, 2017). Sediment transport primarily occurred between the months of January and March. In both tributaries, grain-size distributions of suspended sediment were predominantly coarse-sized sand and were finer than the remnant bed material. Both creeks demonstrate backwater effects from the San Joaquin River, but the more tortuous stream channel and historical mining pits within Little Dry Creek provide more capacity for sediment storage compared to the less complex stream network of Cottonwood Creek. Because loads were computed based on upstream streamgages and not at the confluence of each tributary to the San Joaquin River, annual load estimates do not represent direct flux into the San Joaquin River; instead, these results indicated that in Little Dry Creek, particularly, the lowest portion of the watershed stores sediment before it reaches the San Joaquin River.

California↗
USGS2025

Rice cultivation supports growth and survival of a threatened semi-aquatic reptile

Integration of agroecosystems and other working landscapes with protected lands and waters is critical to the conservation of Earth's biodiversity. Rice agroecosystems support many species by providing aquatic habitat where natural wetlands have been altered or drained. In regions with long dry seasons, rice fields and associated irrigation canals provide essential habitat for wetland-dependent species. We quantified the spatial scale and magnitude of the effect of rice growing on the growth and survival of the giant gartersnake ( Thamnophis gigas ), a threatened species that persists primarily in areas of rice agriculture in the Central Valley of California, USA. We used structural causal models to identify drought condition as a key confounder to adjust for when estimating the total effect of rice growing on demographic rates. We analyzed capture-mark-recapture data from 19 populations of giant gartersnakes with an integrated growth–survival model and used distance-weighted covariates to account for the decline in influence of rice with increasing distance from our study sites. We found strong support for a positive effect of rice grown within 1.9 km of a canal on giant gartersnake growth. There was also support for a positive effect of rice on giant gartersnake survival, although the spatial scale extended out to 5 km or more. Our results demonstrate how active rice growing benefits giant gartersnakes inhabiting irrigation canals and demonstrate an approach for studying landscape effects on wildlife in agroecosystems.

California↗
USGS2025

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

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

Open-File Report↗
USGS2015

Geomorphic, flood, and groundwater-flow characteristics of Bayfield Peninsula streams, Wisconsin, and implications for brook-trout habitat

In 2002–03, the U.S. Geological Survey conducted a study of the geomorphic, flood, and groundwater-flow characteristics of five Bayfield Peninsula streams, Wisconsin (Cranberry River, Bark River, Raspberry River, Sioux River, and Whittlesey Creek) to determine the physical limitations for brook-trout habitat. The goals of the study were threefold: (1) to describe geomorphic characteristics and processes, (2) to determine how land-cover characteristics affect flood peaks, and (3) to determine how regional groundwater flow patterns affect base flow. The geomorphic characterization consisted of analyses of historical aerial photographs and General Land Office Survey notes, observations from helicopter video footage, surveys of valley cross sections, and coring. Sources of sediment were identified from the helicopter video and field surveys, and past erosion-control techniques were evaluated. Geomorphic processes, such as runoff sediment erosion, transport, and deposition, are driven by channel location within the drainage network, texture of glacial deposits, and proximity to postglacial lake shorelines; these processes have historically increased because of decreases in upland forest cover and channel roughness. Sources of sediment for all studied streams mainly came from bank, terrace, or bluff erosion along main stem reaches and along feeder tributaries that bisect main-stem entrenched valley sides. Bluff, terrace, and bank erosion were the major sources of sediment to Whittlesey Creek and the Sioux River. No active bluff erosion was observed on the Cranberry River or the Bark River but anecdotal information suggests that landslides occasionally happen on the Cranberry River. For the Bark River, sources of sediment were somewhat evenly divided among road crossings (bridges, culverts, and unimproved forest lanes), terrace erosion, bank erosion, and incision along upper main stems and feeder channels along valley sides. Evaluation of past erosion-control techniques indicated that bluffs were stabilized by a combination of artificial hardening and bioengineering of the bluff base and reducing mass wasting of the tops of the bluffs. Flood hydrographs for the Cranberry River were simulated for four land-cover scenarios—late 20th century (1992–93), presettlement (before 1870), peak agriculture (1928), and developed (25 percent urban). Results were compared to previous simulations of flood peaks for Whittlesey Creek and for North Fish Creek (southern adjacent basin to Whittlesey Creek). Even though most uplands are presently forested, flood peaks simulated for 1992–93 were 1.5 to 2 times larger than presettlement flood peaks. The increased flood peaks caused (1) increased incision along upper main stems and tributaries that bisect entrenched valley sides, (2) bluff and terrace erosion along reaches with entrenched valleys, (3) overbank deposition and bar formation in middle and lower main stems, and (4) aggradation in mouth areas. A base-flow survey was conducted and a groundwater-flow model was developed for the Bayfield Peninsula to delineate groundwater contributing areas. A deep aquifer system, which includes thick deposits of sand and the upper part of the bedrock, is recharged through the permeable sands in the center of the peninsula. Base flow is unevenly distributed among the Bayfield streams and depends on the amount of channel incision and the proximity of the channels to the recharge area and coarse outwash deposits. Groundwater contributing areas for the five streams do not coincide with surface-water-contributing areas. About 89 percent of total recharge to the deep aquifer system discharges to Bayfield streams; the remaining 11 percent directly discharges to Lake Superior. Historical land-cover changes have had negligible effects on groundwater-flow from the deep aquifer system. Available brook-trout habitat is dependent on the locations of groundwater upwellings, the sizes of flood peaks, and sediment loads. Management practices that focus on reducing or slowing runoff from upland areas and increasing channel roughness have potential to reduce flood peaks, erosion, and sedimentation and improve brook-trout habitat in all Bayfield Peninsula streams.

Wisconsin↗
USGS2015

Hydraulic, geomorphic, and trout habitat conditions of the Lake Fork of the Gunnison River in Hinsdale County, Lake City, Colorado, Water Years 2010-2011

Channel rehabilitation, or reconfiguration, to mitigate a variety of riverine problems has become a common practice in the western United States. However, additional work to monitor and assess the channel response to, and the effectiveness of, these modifications over longer periods of time (decadal or longer) is still needed. The Lake Fork of the Gunnison River has been an area of active channel modification to accommodate the needs of the Lake City community since the 1950s. The Lake Fork Valley Conservancy District began a planning process to assess restoration options for a reach of the Lake Fork in Lake City to enhance hydraulic and ecologic characteristics of the reach. Geomorphic channel form is affected by land-use changes within the basin and geologic controls within the reach. The historic channel was defined as a dynamic, braided channel with an active flood plain. This can result in a natural tendency for the channel to braid. A braided channel can affect channel stability of reconfigured reaches when a single-thread meandering channel is imposed on the stream. The U.S. Geological Survey, in cooperation with the Colorado Water Conservation Board and Colorado River Water Conservation District, began a study in 2010 to quantify existing hydraulic and habitat conditions for a reach of the Lake Fork of the Gunnison River in Lake City, Colorado. The purpose of this report is to quantify existing Lake Fork hydraulic and habitat conditions and establish a baseline against which post-reconfiguration conditions can be compared. This report (1) quantifies the existing hydraulic and geomorphic conditions in a 1.1-kilometer section of the Lake Fork at Lake City that has been proposed as a location for future channel-rehabilitation efforts, (2) characterizes the habitat suitability of the reach for two trout species based on physical conditions within the stream, and (3) characterizes the current riparian canopy density. The FaSTMECH computational flow-model within MD_SWMS was selected to characterize the effects of streamflow on hydraulic and habitat-suitability conditions for a study reach of the Lake Fork. Habitat suitability was evaluated for cutthroat ( Oncorhynchus clarkii ) and brown trout ( Salmo trutta morpha fario ) fry, juveniles, and adults. Microscale (point locations) and mesoscale (reach features) habitats were assessed using the combination of field observations, measurements, and hydraulic simulations within the study reach of the Lake Fork. Microscale trout habitat, presented as weighted usable area, generally increased as streamflow increased for both trout species and all life stages. Areas of suitable microscale habitat occur along the banks for flows of 900 cubic feet per second (ft 3 /s) and less. Out-of-bank areas became more substantial contributors to overall habitat availability for flows of 1,300 ft 3 /s or more when compared to other features. Adult habitat, for both trout species, was the most abundant habitat type for nearly all streamflows. In general, the upper reach provided 2–3 times more available habitat than the lower reach for both trout species. Mesoscale trout habitat of the Lake Fork was assessed based on the conditions present in the 150 ft 3 /s flow simulation as well as field observation. Both the upper and lower reach is primarily characterized as riffle/run habitat. The presence of pool habitat was limited throughout both reaches and occurred along the channel margins. For both reaches, the pool habitat was less than 5 percent of the total wetted area, a percentage that is substantially lower than the recommendations for sustainable populations of 40–70 percent. Areas of cover were adjacent to potential drift feeding areas in the lower reach, and often occurred within the same pool habitat. This may favor energy expenditure ratios of both fish species, wherein little energy is needed to acquire adequate food sources. Sediment mobility is an important process for flushing fine sediments from within the gravel frameworks. Evaluations of channel and flow characteristics at cross-section locations 2–8 show a range of streambed mobility. In general, boundary shear stress and streambed mobility increase with increases in streamflow. Within the cross sections, the greatest boundary shear stress occurs towards the center of the channel. Reach-scale assessment of sediment mobility in the lower reach shows increased streambed mobility. This is due in part to smaller grain sizes in the lower reach, but may also reflect the greater extent of channel alterations, specifically the temporary berms constructed by CDOT in the late 1980s and 1990s, present in this reach.

Colorado↗
USGS2010

Population structure and genetic diversity of greater sage-grouse (Centrocercus urophasianus) in fragmented landscapes at the northern edge of their range

Range-edge dynamics and anthropogenic fragmentation are expected to impact patterns of genetic diversity, and understanding the influence of both factors is important for effective conservation of threatened wildlife species. To examine these factors, we sampled greater sage-grouse ( Centrocercus urophasianus ) from a declining, fragmented region at the northern periphery of the species’ range and from a stable, contiguous core region. We genotyped 2,519 individuals at 13 microsatellite loci from 104 leks in Alberta, Saskatchewan, Montana, and Wyoming. Birds from northern Montana, Alberta, and Saskatchewan were identified as a single population that exhibited significant isolation by distance, with the Milk River demarcating two subpopulations. Both subpopulations exhibited high genetic diversity with no evidence that peripheral regions were genetically depauperate or highly structured. However, river valleys and a large agricultural region were significant barriers to dispersal. Leks were also composed primarily of non-kin, rejecting the idea that leks form because of male kin association. Northern Montana sage-grouse are maintaining genetic connectivity in fragmented and northern peripheral habitats via dispersal through and around various forms of fragmentation.

Alberta, Saskatchewan, Montana, Wyoming↗
USGS2008

Population dynamics of the Concho water snake in rivers and reservoirs

The Concho Water Snake ( Nerodia harteri paucimaculata ) is confined to the Concho–Colorado River valley of central Texas, thereby occupying one of the smallest geographic ranges of any North American snake. In 1986, N. h. paucimaculata was designated as a federally threatened species, in large part because of reservoir projects that were perceived to adversely affect the amount of habitat available to the snake. During a ten-year period (1987–1996), we conducted capture–recapture field studies to assess dynamics of five subpopulations of snakes in both natural (river) and man-made (reservoir) habitats. Because of differential sampling of subpopulations, we present separate results for all five subpopulations combined (including large reservoirs) and three of the five subpopulations (excluding large reservoirs). We used multistate capture–recapture models to deal with stochastic transitions between pre-reproductive and reproductive size classes and to allow for the possibility of different survival and capture probabilities for the two classes. We also estimated both the finite rate of increase (λ) for a deterministic, stage-based, female-only matrix model using the average litter size, and the average rate of adult population change, λ ˆ, which describes changes in numbers of adult snakes, using a direct capture–recapture approach to estimation. Average annual adult survival was about 0.23 and similar for males and females. Average annual survival for subadults was about 0.14. The parameter estimates from the stage-based projection matrix analysis all yielded asymptotic values of λ < 1, suggesting populations that are not viable. However, the direct estimates of average adult λ for the three subpopulations excluding major reservoirs were λ ˆ = 1.26, SE ˆ(λ ˆ) = 0.18 and λ ˆ = 0.99, SE ˆ(λ ˆ) = 0.79, based on two different models. Thus, the direct estimation approach did not provide strong evidence of population declines of the riverine subpopulations, but the estimates are characterized by substantial uncertainty.

Copeia↗
USGS2015

Sampling to estimate population size and detect trends in Tricolored Blackbirds

The Tricolored Blackbird ( Agelaius tricolor ) is a medium-sized passerine that nests in the largest colonies of any North American landbird since the extinction of the passenger pigeon ( Ectopistes migratorius ) over 100 years ago (Beedy and Hamilton 1999). The species has a restricted range that occurs almost exclusively within California, with only a few hundred birds scattered in small groups in Oregon, Washington, Nevada, and northwestern Baja California, Mexico (Beedy and Hamilton 1999). Tricolored Blackbirds are itinerant breeders (i.e., breed more than once per year in different locations) and use a wide variety of nesting substrates (Hamilton 1998), many of which are ephemeral. They are also insect dependent during the breeding season, and reproductive success is strongly correlated with relative insect abundance (Meese 2013). Researchers have noted for decades that Tricolored Blackbird’s insect prey are highly variable in space and time; Payne (1969), for example, described the species as a grasshopper follower because they are preferred food items, and high grasshopper abundance is often associated with high reproductive success (Payne 1969, Meese 2013). Thus, the species’ basic reproductive strategy is tied to rather infrequent periods of relatively high insect abundance in some locations followed by much longer periods of range -wide relatively low insect abundance and poor reproductive success. Of course, anthropogenic factors such as habitat loss and insecticide use may be at least partly responsible for these patterns (Hallman et al. 2014, Airola et al. 2014).

Central Valley Bird Club Bulletin↗
USGS1998

Water-quality assessment of the lower Illinois River Basin: Environmental setting

The lower Illinois River Basin (LIRB) encompasses 18,000 square miles of central and western Illinois. Historical and recent information from Federal, State, and local agencies describing the physiography, population, land use, soils, climate, geology, streamflow, habitat, ground water, water use, and aquatic biology is summarized to describe the environmental setting of the LIRB. The LIRB is in the Till Plains Section of the Central Lowland physiographic province. The basin is characterized by flat topography, which is dissected by the Illinois River. The drainage pattern of the LIRB has been shaped by many bedrock and glacial geologic processes. Erosion prior to and during Pleistocene time created wide and deep bedrock valleys. The thickest deposits and most major aquifers are in buried bedrock valleys. The Wisconsinan glaciation, which bisects the northern half of the LIRB, affects the distribution and characteristics of glacial deposits in the basin. Agriculture is the largest land use and forested land is the second largest land use in the LIRB. The major urban areas are near Peoria, Springfield, Decatur, and Bloomington-Normal. Soil type and distribution affect the amount of soil erosion, which results in sedimentation of lakes and reservoirs in the basin. Rates of soil erosion of up to 2 percent per year of farmland soil have been measured. Many of the 300 reservoirs, lakes, and wetlands are disappearing because of sedimentation resulting from agriculture activities, levee building, and urbanization. Sedimentation and the destruction of habitat appreciably affect the ecosystem. The Illinois River is a large river-floodplain ecosystem where biological productivity is enhanced by annual flood pulses that advance and retreat over the flood plain and temporarily expand backwater and flood-plain lakes. Ground-water discharge to streams affects the flow and water quality of the streams. The water budget of several subbasins show variability in ground-water contribution from runoff and storage. More than half of the drinking water, including domestic and public-supply use, in the LIRB is from ground water. Fifty-two percent of the public-supply water is from surface water. Ground-water withdrawals mostly are from glacial sand and gravel aquifers. Structural features, such as monoclines, synclines, and anticlines, in the buried bedrock affect the water quality of the aquifers. There are five natural environmental divisions in the LIRB. The Grand Prairie covers most of the northeastern half of the basin, and the Western Forest-Prairie covers most of the southwestern half. Implications of environmental setting for water quality in the LIRB are related primarily to land use. The balanced fish community indicates that the lower Illinois River is affected less from urban and industrial waste than the upper Illinois River. A decrease in dissolved oxygen concentrations and turbidity in the lower reaches of the basin in 1993 have resulted from the recent influx of European zebra mussels to the LIRB. Many factors affect water quality in the LIRB. Bedrock and surface topography, type of glacial material, and land use most directly affect water quality in the basin.

Illinois↗
USGS2008

Mercury geochemistry of gold placer tailings, sediments, bedrock, and waters in the lower Clear Creek area, Shasta County, California— Report of investigations, 2001-2003

Clear Creek, one of the major tributaries of the upper Sacramento River, drains the eastern Trinity Mountains. Alluvial plain and terrace gravels of lower Clear Creek, at the northwest edge of the Sacramento Valley, contain placer gold that has been mined since the Gold Rush by various methods including hydraulic mining and dredging. In addition, from the 1950s to the 1980s aggregate-mining operations removed gravel from the lower Clear Creek flood plain. Since Clear Creek is an important stream for salmon production, a habitat restoration program is underway to repair damage from mining and improve conditions for spawning. This program includes moving dredge tailings to increase the area of spawning gravel and to fill gravel pits in the flood plain, raising the concern that mercury lost to these tailings in the gold recovery process may be released and become available to biota. The purposes of our study are to identify sources, transport, and dispersal of mercury in the lower Clear Creek area and identify environments in which bioavailable methylmercury is produced. Analytical data acquired include total mercury and methylmercury concentrations in sediments, tailings, and water. Mercury concentrations in bedrock and unmined gravels in and around the mined area are low and are taken to represent background concentrations. Bulk mercury values in placer mining tailings range from near-background in coarse dry materials to more than 40 times background in sands and silts exposed to mercury in sluices. Tailings are entrained in flood-plain sediments and active stream sediments; consequently, mercury concentrations in these materials range from background to about two to three times background. Mercury in sediments and tailings is associated with fine size fractions. The source of most of this mercury is historical gold mining in the Clear Creek watershed. Although methylmercury levels are low in most of these tailings and sediments, flood-plain sediment in shallow flood-plain ponds, tailings in a dredge pond, and active stream sediment in a Clear Creek backwater have elevated levels of methylmercury. Stream waters in the area show low mercury levels during both summer and winter base-flow conditions. During winter high flows total mercury increases by about one order of magnitude; this additional mercury is associated with suspended particulate material. Methylmercury is low in stream waters. Ponds in various environments generally have higher total mercury levels in waters than Clear Creek under base-flow conditions and higher methylmercury levels in both sediments and waters. Ponds are probably the main source of bioavailable mercury in the lower Clear Creek area. Several saline springs occur in the area. The saline waters are enriched in lithium, boron, and mercury, similar to connate waters that are expelled along thrust faults to the south on the west side of the Sacramento Valley. Saline springs may locally contribute some mercury to pond and drainage waters.

California↗
USGS2020

Coal-mining intensity influences species and trait distributions of stream fishes in two Central Appalachian watersheds

Documenting responses of biotic assemblages to coal-mining impacts is crucial to informing regulatory and reclamation actions. However, attributing biotic patterns to specific stressors is difficult given the dearth of preimpact studies and prevalence of confounding factors. Analysing species distributions and abundances, especially stratified by species traits, provides insights into how assemblage composition shifts occur. We evaluated stream habitats and fish assemblages along a mining intensity gradient in 83 headwater (2nd- and 3rd-order) streams of the upper Clinch and Powell river basins in Virginia. Our multivariate gradient (MINE.PC1) was based on percentages of watershed area covered by surface mine, underground mine and valley fill to represent spatial variance in mining intensity. MINE.PC1 was positively correlated with conductivity and percentage of substrate as cobble. Forty fish-assemblage metrics were analysed via boosted regression trees to assess assemblage responses to mining intensity, while accounting for environmental variation and spatial structure among sites. Conductivity and MINE.PC1 were strongly negatively related to occurrences of Fantail Darter ( Etheostoma flabellare ) and sculpin ( Cottus ) spp. Several taxonomic, trophic and reproductive metrics of assemblage composition responded strongly to mining intensity or its instream correlates. For example, coal mining favoured omnivore-herbivores, but inhibited invertivores, simple lithophils and nonsimple nonlithophils. We revealed distinct negative and positive responses to mining-related stressors, which suggest changes to macroinvertebrate prey availability and/or contaminant loads contribute to fish extirpations in coalfield streams. Future assessments of mining impacts on fish assemblages could be more instructive by including characterisations of physicochemical stressors and regionally calibrated biotic metrics with demonstrated sensitivity to mining.

Virginia↗
USGS2026

Recent scientific contributions by the U.S. Geological Survey in the San Francisco Bay and Sacramento–San Joaquin Delta Estuary

Introduction The San Francisco Bay and Sacramento–San Joaquin Delta Estuary (hereafter, Bay-Delta) is the largest estuary on the West Coast of the United States. The Bay-Delta covers more than 1,600 square miles and drains a watershed of more than 75,000 square miles, which is greater than 40 percent of California. The region surrounding the Bay-Delta is home to about 10 million people, and its habitats (fig. 1) support more than 800 plant and animal species. The waterways of the Bay-Delta are the central hub of California’s extensive freshwater delivery system, supplying water to more than 27 million Californians and 4 million acres of farmland in the Central Valley. The U.S. Geological Survey (USGS) is the primary science agency of the U.S. Department of the Interior, providing a broad range of Earth, water, biological, and mapping data and expertise to inform natural resource management across the country. This fact sheet focuses on research conducted by the USGS in the Bay-Delta region, mostly within the past 5 years. The fact sheet is organized across five major themes: water flow and water quality, fish and wildlife, wetland restoration, invasive species, and hazards. In each of these areas, the USGS works closely with Federal, State, and local agencies; academia; and non-governmental organizations to provide objective, evidence-based science. The data and knowledge gained from USGS research and monitoring are publicly available and are routinely used by agencies, including the U.S. Bureau of Reclamation, U.S. Army Corps of Engineers, U.S. Fish and Wildlife Service, California Department of Water Resources, California Department of Fish and Wildlife, California State Water Resources Control Board, Delta Stewardship Council, and many additional organizations and stakeholders to inform management of the Bay-Delta region and its resources.

California↗
USGS2020

Groundwater characterization and effects of pumping in the Death Valley regional groundwater flow system, Nevada and California, with special reference to Devils Hole

Groundwater flow and development were characterized in four groundwater basins of the Death Valley regional flow system in Nevada and California with calibrated, groundwater-flow models. Natural groundwater discharges in the Furnace Creek, Lower Amargosa, and Saratoga Spring areas were defined and distributed consistently with a revised hydrogeologic framework. This simplified hydrogeologic framework was limited to four hydraulically unique, hydrogeologic units: (1) basin fill; (2) carbonate rocks; (3) volcanic rocks; and (4) low-permeability granitic and siliciclastic rocks. Hydrogeologic units and division of carbonate and volcanic rocks between shallow and deep were supported by results from 271 aquifer tests and specific-capacity estimates. Greater than 90 percent of field-estimated transmissivity occurred within 1,600 feet (ft) of the water table. Pumping in the study area from 1960 to 2010 averaged 46,000 acre-feet per year (acre-ft/yr), which is 80 percent of the predevelopment discharge. The central Amargosa Desert and Pahrump Valley were the two primary pumping centers and measurably affected water levels across 900 square miles in 2018. Water levels in Devils Hole were a special focus because endangered Devils Hole pupfish ( Cyprinodon diabolis ) are affected by water-level declines. Pumping 42,100 acre-ft by Cappaert Enterprises, formerly Spring Meadows, Inc., caused a 2.3-ft water-level decline in Devils Hole , which temporarily reduced habitat of Devils Hole pupfish by 85 percent in 1972. If no pumping occurred, water levels in Devils Hole would have risen naturally about 1 ft between 1973 and 2018 from temporal variations in recharge. The 2.6-ft range of measured water-level changes in Devils Hole was simulated with a root-mean-square error of 0.2 ft during the 70-year period of record. Simulated water-level declines from pumping totaled 1.4 ft in 2018, with 25 and 34 percent attributed to pumping by Cappaert Enterprises and the central Amargosa Desert, respectively. Water levels in Devils Hole will decline at rates of 0.1–0.2 ft per decade if pumping from Ash Meadows groundwater basin and the central Amargosa Desert continue at current rates. Effects of future natural water-level fluctuations remain unknown. Ash Meadows and Alkali Flat–Furnace Creek Ranch groundwater basins are hydraulically connected near well AD-4 , about 5 miles south of the town of Amargosa Valley, Nevada. About 40 percent of the discharge from the Furnace Creek area is recharged in the Ash Meadows groundwater basin. Basin fill in the central Amargosa Desert hydraulically connects carbonate rocks east of well AD-4 with saturated carbonate rocks in the Funeral Range. About 7 percent of the 960,000 acre-ft pumped from Ash Meadows and Alkali Flat–Furnace Creek Ranch groundwater basins prior to 2019 was captured discharge from springs and phreatophytes. Greater than 40 percent of the 2,080,000 acre-ft pumped from Pahrump Valley between 1910 and 2019 was capture that primarily discharged from Bennetts and Manse Springs. Simulated advective-flow distances and velocities from underground nuclear tests are within the range of advective transport calculations from tritium data and previous radionuclide transport investigations. Boundary conditions and flow rates from the regional model in this study are plausible for local-scale flow and radionuclide transport models. Simulated 165-year groundwater-flow paths do not extend into pumping areas and effects of regional pumping on advective transport are negligible.

California, Nevada↗
USGS2016

Object-based forest classification to facilitate landscape-scale conservation in the Mississippi Alluvial Valley

The Mississippi Alluvial Valley is a floodplain along the southern extent of the Mississippi River extending from southern Missouri to the Gulf of Mexico. This area once encompassed nearly 10 million ha of floodplain forests, most of which has been converted to agriculture over the past two centuries. Conservation programs in this region revolve around protection of existing forest and reforestation of converted lands. Therefore, an accurate and up to date classification of forest cover is essential for conservation planning, including efforts that prioritize areas for conservation activities. We used object-based image analysis with Random Forest classification to quickly and accurately classify forest cover. We used Landsat band, band ratio, and band index statistics to identify and define similar objects as our training sets instead of selecting individual training points. This provided a single rule-set that was used to classify each of the 11 Landsat 5 Thematic Mapper scenes that encompassed the Mississippi Alluvial Valley. We classified 3,307,910&plusmn;85,344 ha (32% of this region) as forest. Our overall classification accuracy was 96.9% with Kappa statistic of 0.96. Because this method of forest classification is rapid and accurate, assessment of forest cover can be regularly updated and progress toward forest habitat goals identified in conservation plans can be periodically evaluated.

Arkansas, Louisiana, Mississippi, Missouri↗
USGS2009

Channel change and bed-material transport in the Lower Chetco River, Oregon

The lower Chetco River is a wandering gravel-bed river flanked by abundant and large gravel bars formed of coarse bed-material sediment. The large gravel bars have been a source of commercial aggregate since the early twentieth century for which ongoing permitting and aquatic habitat concerns have motivated this assessment of historical channel change and sediment transport rates. Analysis of historical channel change and bed-material transport rates for the lower 18 kilometers show that the upper reaches of the study area are primarily transport zones, with bar positions fixed by valley geometry and active bars mainly providing transient storage of bed material. Downstream reaches, especially near the confluence of the North Fork Chetco River, have been zones of active sedimentation and channel migration. Multiple analyses, supported by direct measurements of bedload during winter 2008–09, indicate that since 1970 the mean annual flux of bed material into the study reach has been about 40,000–100,000 cubic meters per year. Downstream tributary input of bed-material sediment, probably averaging 5–30 percent of the influx coming into the study reach from upstream, is approximately balanced by bed-material attrition by abrasion. Probably very little bed material leaves the lower river under natural conditions, with most of the net influx historically accumulating in wider and more dynamic reaches, especially near the North Fork Chetco River confluence, 8 kilometers upstream from the Pacific Ocean. The year-to-year flux, however, varies tremendously. Some years probably have less than 3,000 cubic meters of bed-material entering the study area; by contrast, some high-flow years, such as 1982 and 1997, likely have more than 150,000 cubic meters entering the reach. For comparison, the estimated annual volume of gravel extracted from the lower Chetco River for commercial aggregate during 2000–2008 has ranged from 32,000 to 90,000 cubic meters and averaged about 59,000 cubic meters per year. Mined volumes probably exceeded 140,000 cubic meters per year for several years in the late 1970s. Repeat surveys and map analyses indicate a reduction in bar area and sinuosity between 1939 and 2008, chiefly in the period 1965–95. Repeat topographic and bathymetric surveys show channel incision for substantial portions of the study reach, with local areas of bed lowering by as much as 2 meters. A specific gage analysis at the upstream end of the study reach indicates that incision and narrowing followed aggradation culminating in the late 1970s. These observations are all consistent with a reduction of sediment supply relative to transport capacity since channel surveys in the late 1970s, probably owing to a combination of (1) bed-sediment removal and (2) transient river adjustments to large sediment volumes brought by floods such as those in 1964, and to a lesser extent, 1996.

Open-File Report↗
USGS2010

Channel change and bed-material transport in the Lower Chetco River, Oregon

The lower Chetco River is a wandering gravel-bed river flanked by abundant and large gravel bars formed of coarse bed-material sediment. Since the early twentieth century, the large gravel bars have been a source of commercial aggregate for which ongoing permitting and aquatic habitat concerns have motivated this assessment of historical channel change and sediment transport rates. Analysis of historical channel change and bed-material transport rates for the lower 18 kilometers shows that the upper reaches of the study area are primarily transport zones, with bar positions fixed by valley geometry and active bars mainly providing transient storage of bed material. Downstream reaches, especially near the confluence of the North Fork Chetco River, are zones of active sedimentation and channel migration. Multiple analyses, supported by direct measurements of bedload during winter 2008–09, indicate that since 1970 the mean annual flux of bed material into the study reach has been about 40,000–100,000 cubic meters per year. Downstream tributary input of bed-material sediment, probably averaging 5–30 percent of the influx coming into the study reach from upstream, is approximately balanced by bed-material attrition by abrasion. Probably little bed material leaves the lower river under natural conditions, with most net influx historically accumulating in wider and more dynamic reaches, especially near the North Fork Chetco River confluence, 8 kilometers upstream from the Pacific Ocean. The year-to-year flux, however, varies tremendously. Some years may have less than 3,000 cubic meters of bed material entering the study area; by contrast, some high-flow years, such as 1982 and 1997, likely have more than 150,000 cubic meters entering the reach. For comparison, the estimated annual volume of gravel extracted from the lower Chetco River for commercial aggregate during 2000–2008 has ranged from 32,000 to 90,000 cubic meters and averaged about 59,000 cubic meters per year. Mined volumes probably exceeded 140,000 cubic meters per year for several years in the late 1970s. Repeat surveys and map analyses indicate a reduction in bar area and sinuosity between 1939 and 2008, chiefly in the period 1965–95. Repeat topographic and bathymetric surveys show channel incision for substantial portions of the study reach, with local areas of bed lowering by as much as 2 meters. A specific gage analysis at the upstream end of the study reach indicates that incision and narrowing followed aggradation culminating in the late 1970s. These observations are all consistent with a reduction of sediment supply relative to transport capacity since channel surveys in the late 1970s, probably owing to a combination of (1) bed sediment removal and (2) transient river adjustments to large sediment volumes brought by floods such as those in 1964 and, to a lesser extent, 1996.

Oregon↗
USGS2014

Synthesis of thirty years of surface water quality and aquatic biota data in Shenandoah National Park: Collaboration between the US Geological Survey and the National Park Service

The eastern United States has been the recipient of acidic atmospheric deposition (hereinafter, “acid rain”) for many decades. Deleterious effects of acid rain on natural resources have been well documented for surface water (e.g., Likens et al. 1996; Stoddard et al. 2001), soils (Bailey et al. 2005), forest health (Long et al. 2009), and habitat suitability for stream biota (Baker et al. 1993). Shenandoah National Park (SNP) is located in northern and central Virginia and consists of a long, narrow strip of land straddling the Blue Ridge Mountains (Figure 1). The park’s elevated topography and location downwind of the Ohio River valley, where many acidic emissions to the atmosphere are generated (NSTC 2005), have made it a target for acid rain. Characterizing the link between air quality and water quality as related to acid rain, contaminants, soil conditions, and forest health is a high priority for research and monitoring in SNP. The US Geological Survey (USGS) and SNP have had a long history of collaboration on documenting acid rain effects on the park’s natural resources, starting in 1985 and continuing to the present (Lynch and Dise 1985; Rice et al. 2001, 2004, 2005, 2007; Deviney et al. 2006, 2012; Jastram et al. 2013).

Virginia↗
USGS2007

Investigation of wind and water level for the Giacomini Wetland Restoration Project, Point Reyes National Seashore

Point Reyes National Seashore (PRNS), comprising unique elements of geological, biological, and historical interest, is located on the central California coast approximately 60 km northwest of San Francisco. The National Seashore contains nearly 130 km of exposed and protected shorelines, spectacular coastal cliffs and headlands, lagoons, open grasslands, bushy hillsides, and forested ridges. Approximately 30 km of the shoreline are coastal-dune habitat that supports 11 federally listed species, including the threatened western snowy plover and the endangered plants Tidestrom's lupine ( Lupinus tidestromii ) and beach layia ( Layia carnosa ). The San Andreas Fault, a right-lateral strike-slip fault, trends northwest along the northeastern side of the park. Tomales Bay, which is straight, long, narrow, and shallow, runs along the northeastern boundary of PRNS. The Bay, which fills the northwestern end of a rift valley at the intersection of the San Andreas Fault with the coastline, is approximately 20 km long, 2 km wide, and 6 m deep with mountainous terrain to the southwest and rolling hills to the northeast. Tomales Bay is one of the cleanest estuaries on the West Coast. In winter, approximately 17,000 to 20,000 shorebirds inhabit Tomales Bay and Bodega Bay, which lies directly to the north. At the head of Tomales Bay, the Giacomini Ranch comprises 563 acres of pastureland currently being used for grazing dairy cattle. After more than 50 years of operation as a dairy, the National Park Service acquired the Giacomini property with the intention to restore most of it and the nearby Olema Marsh to tidal wetland. Restoration will add approximately 4% to the existing coastal wetlands in California. The project will return the headwaters of Tomales Bay and two major stream intersections to an intertidal marsh environment, enhancing habitat for both wildlife and fish populations and contributing to the long-term health of Tomales Bay. Prior to the establishment of the ranch, the area was primarily salt marsh that formed as the delta of Lagunitas Creek expanded into Tomales Bay. In converting the salt marsh to dairy land, levees and tide gates were constructed to prevent tidal incursion and stream flooding. Those levees have significantly altered the patterns of estuarine circulation and sediment deposition. To restore natural hydrologic processes within the area and to promote the return of ecological functions and processes, the levees will have to be breached or removed. Developing a successful restoration strategy requires knowledge of elevations within the pastureland and the range of water depths that can be expected from tidal, river, and wind action. In support of the restoration program, the USGS provides technical assistance to PRNS in the form of a scientific study focusing on understanding the physical processes that could affect the Giacomini wetland restoration. The study will yield scientific products that NPS resource managers can use in designing and implementing the restoration project. Research elements include: - Develop a Geodetic Control Network (GCN) throughout PRNS that meets the standards specified National Geodetic Survey data base (the NGS "Bluebook"). The grid will allow this and future studies to be conducted to a precision commensurate with the expressed goals of PRNS. The survey will consist of three steps: (1) verify existing GPS control monuments in the area; (2) tie control monuments in the study areas to the GPS control monuments; and (3) establish NAVD88 elevations using a digital electronic level. - Conduct a detailed survey of the Giacomini site to produce an accurate topographic map of the property. The site survey can be coupled with on-site water-level measurements to produce an empirical flooding model. - Measure water level and wind regime at the Giacomini site. The water-level range is critical to determining the wetland types based on the elevation of the dairy land. Water level at Sacramento Landing, in central Tomales Bay, will also be measured for comparison. As of November 2005, we have created a GCN, produced a detailed topographic map of the Giacomini site, and collected approximately three years of water-level and wind data at the Giacomini site and over one year of usable water-level data at the Sacramento Landing pier.

California↗