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At least 793 records · Page 44Linked to original sources

USGS1983

Assessment of gray whale feeding grounds and sea floor interaction in the northeastern Bering Sea

A dense ampeliscid amphipod community in Chirikov Basin and around St. Lawrence Island in the northeastern Bering Sea has been outlined by summarizing biological studies, analyzing bioturbation in sediment samples, and examining sea floor photos and videotapes. The amphipod population is associated with a homogeneous, relict fine-grained sand body 0.10-1.5 m thick that is deposited during the marine transgression over the Bering land bridge 8,000-10,000 yr B.P. Modern current and water mass movements and perhaps whale feeding activity prevent modern deposition in this area. The distribution of the transgressive sand sheet, associated amphipod community and feeding gray whales mapped by aerial survey correlate closely with three types of sea-floor pits observed on high (500 kHz) and low (105 kHz) resolution side-scan sonar; they are attributed to gray whale feeding traces and their subsequent current scour modification. The fresh and modified feeding pits are present in 22,000 km2 of the basin and they cover a total of 2 to 18% of the sea floor in different areas of the feeding region. The smallest size class of pits approximates whale mouth gape size and is assumed to represent fresh whale feeding pits. Fresh feeding disturbance of the sea floor is estimated to average about 5.7% for a full feeding season. Combined with information that 34% of the measured benthic biomass is amphipod prey species, and calculating the number of gray whale feeding days in the Alaskan waters plus amount consumed per day, it can be estimated that Chirikov Basin, 2% of the feeding area, supplies a minimum of 5.3 to 7.1% of the gray whale's food resource in the Bering Sea and Arctic Ocean. If a maximum of 50% of the fresh feeding features are assumed to be missed because they parallel side-scan beam paths, then a maximum whale food resource of 14.2% is possible in northeastern Bering Sea. Because of side-scan techniques and possible higher amphipod biomass estimates, a reasonable minimum estimate of the total whale food resource in northeastern Bering Sea is 10%. These data show that side-scan sonar is a powerful new technique for analyzing marine mammal benthic feeding grounds. Sonographs reveal that the gray whales profoundly disturb the substrate and initiate substantial further erosion by bottom currents, all of which enhances productivity of the prey species and results in a 'farming of the sea floor'. In turn, because of the high concentration of whale prey species in a prime feeding ground that is vulnerable to the development of petroleum and mining for sand, great care is required in the exploitation of these resources in the Chirikov Basin.

Open-File Report↗

USGS2016

Performance evaluation testing of wells in the gradient control system at a federally operated Confined Disposal Facility using single well aquifer tests, East Chicago, Indiana

The U.S. Geological Survey (USGS) performed tests to evaluate the hydrologic connection between the open interval of the well and the surrounding Calumet aquifer in response to fouling of extraction well pumps onsite. Two rounds of air slug testing were performed on seven monitoring wells and step drawdown and subsequent recovery tests on three extraction wells on a U.S. Army Corps of Engineers Confined Disposal Facility (CDF) in East Chicago, Indiana. The wells were tested in 2014 and again in 2015. The extraction and monitoring wells are part of the gradient control system that establishes an inward gradient around the perimeter of the facility. The testing established a set of protocols that site personnel can use to evaluate onsite well integrity and develop a maintenance procedure to evaluate future well performance. The results of the slug test analysis data indicate that the hydraulic connection of the well screen to the surrounding aquifer material in monitoring wells on the CDF and the reliability of hydraulic conductivity estimates of the surrounding geologic media could be increased by implementing well development maintenance. Repeated air slug tests showed increasing hydraulic conductivity until, in the case of the monitoring wells located outside of the groundwater cutoff wall (MW–4B, MW–11B, MW–14B), the difference in hydraulic conductivity from test to test decreased, indicating the results were approaching the optimal hydraulic connection between the aquifer and the well screen. Hydraulic conductivity values derived from successive tests in monitoring well D40, approximately 0.25 mile south of the CDF, were substantially higher than those derived from wells on the CDF property. Also, values did not vary from test to test like those measured in monitoring wells located on the CDF property, which indicated that a process may be affecting the connectivity of the wells on the CDF property to the Calumet aquifer. Derived hydraulic conductivity values from the initial air slug test during the 2015 testing period for MW–11A and MW–14A are an order of magnitude less than those derived from the final test during the 2014 testing period indicating the development of a low conductivity skin between the final test of the 2014 testing period and the beginning of the 2015 testing period that created a decrease in the connection of the monitoring well screen to the surrounding aquifer material. Repeated step drawdown and recovery testing of the extraction wells tested during this study provided results that indicate a slight increase in the development of a skin and a decrease in the connectivity of the extraction wells with the Calumet aquifer. Hydraulic conductivity values obtained from the test results were relatively similar in EW–4B and EW–14A but were substantially lower for EW–11C. This difference may be due to the presence of finer grained silt deposits in the area surrounding well nest 11. Skin factors calculated during the step drawdown and recovery analysis were lowest in EW–11C and relatively similar in EW–4B and EW–14A. Calculated skin factors increased slightly in the analysis of data collected in 2015 from that collected in 2014. Comparisons of the specific-capacity values calculated from well development data collected following extraction well installation to those calculated during the single well aquifer tests at EW–4B, EW–14A and EW–11C indicate that the productivity of extraction wells on the CDF property has diminished since 2008. Values calculated for monitoring wells MW–4A, MW–11A, and MW–14A were used to evaluate the decrease in air slug derived hydraulic conductivity for monitoring wells within the groundwater cutoff wall between testing in 2014 and 2015. Results from testing by this study indicate that implementation of an air slug testing regimen of the monitoring wells that control the gradient control system at the CDF throughout the course of a year may help sustain the connectivity between the monitoring wells and the surrounding aquifer and provide data to evaluate the need for different types of well development approaches to address chemical or biological fouling issues. Repeated step drawdown and recovery testing of the extraction wells tested during this study provided results that indicate a slight increase in the development of a skin and a decrease in the connectivity of the extraction wells with the Calumet aquifer. Implementation of a specific capacity testing regimen can provide data to record and track well condition through time for individual extraction wells. Results from aquifer testing by this study indicate that specific capacity test results, when paired with recovery testing, provide useful data to measure the development of any low conductivity wellbore skin through the skin factors derived for the individual extraction wells. An initial annual schedule of specific capacity and recovery tests would provide sufficient data to identify substantial short-term changes in the operating condition of the extraction wells.

Indiana↗

USGS2002

Physical data and biological data for algae, aquatic invertebrates, and fish from selected reaches on the Carson and Truckee rivers, Nevada and California, 1993-97

This report, a product of the National Water- Quality Assessment Program, is a compilation of physical data and biological data for algae, aquatic invertebrates, and fish collected in the Carson and Truckee River Basins, Nevada and California. Most of the data were collected between 1993 and 1996 at selected reaches on the Carson and Truckee Rivers. Algae and aquatic invertebrate samples were collected from cobble riffles, submerged woody-snag habitats, and from depositional areas such as pools. Between 1993 and 1996, fish and crayfish were collected from all wadeable habitats at each of seven basic-fixed sites using either electroshocking methods or seining. Additional fish and crayfish were collected at one site on the Truckee River in 1997. Fish were identified to species, measured for total and standard length, checked for anomalies, and weighed at the collection site. Fish were returned to the stream after measurements were taken. Measurements of water depth, stream velocity, determinations of substrate type and substrate embeddedness were made at each sampling site. Algae and aquatic invertebrate samples were sent to the U.S. Geological Survey National Water-Quality Laboratory for identification and enumeration. A total of 103 semi-quantitative and 55 qualitative algae samples were collected at 20 river reaches on the Carson and Truckee Rivers between 1993 and 1996. These samples represent algae in cobble riffles, on submerged woody snags, and on sediment surfaces in depositional areas. In those 158 samples, 514 algal species, varieties, or forms were identified. Of the 8 algal phyla represented, the diatoms (Phylum Bacillariophyta) were the most abundant with 351 species, varieties, or forms. The green algae (Phylum Chlorophyta) were next in abundance with 108 species, varieties, or forms followed by the blue-green algae (Phylum Cyanophyta) with 41 species, varieties, or forms. A total of 49 semi-quantitative aquatic invertebrate samples were collected at 27 river reaches on the Carson and Truckee Rivers between 1993 and 1996. These samples represent invertebrates in cobble riffles and on submerged woody snags. In those 49 samples, members of 6 phyla were identified. Roundworms were identified only to phylum (Nematoda) and free-living flatworms and snails were identified only to class (Turbellaria and Gastroda). Organisms were identified as belonging to 19 invertebrate orders. Most of the invertebrates that could be identified to genus or species belonged in the orders Ephemeroptera, Plecoptera, and Trichoptera of the arthropod class Insecta. Fish and crayfish populations in the Carson and Truckee Rivers were sampled 29 times between 1993 and 1997. These collections resulted in the identification of 18 fish species and one endemic crayfish species. Twelve of the 18 fish species identified are not native to the Carson and Truckee River Basins.

Open-File Report↗

USGS2007

A Quantitative Threats Analysis for the Florida Manatee ( Trichechus manatus latirostris )

The Florida manatee (Trichechus manatus latirostris) is an endangered marine mammal endemic to the southeastern United States. The primary threats to manatee populations are collisions with watercraft and the potential loss of warm-water refuges. For the purposes of listing, recovery, and regulation under the Endangered Species Act (ESA), an understanding of the relative effects of the principal threats is needed. This work is a quantitative approach to threats analysis, grounded in the assumption that an appropriate measure of status under the ESA is based on the risk of extinction, as quantified by the probability of quasi-extinction. This is related to the qualitative threats analyses that are more common under the ESA, but provides an additional level of rigor, objectivity, and integration. In this approach, our philosophy is that analysis of the five threat factors described in Section 4(a)(1) of the ESA can be undertaken within an integrated quantitative framework. The basis of this threats analysis is a comparative population viability analysis. This involves forecasting the Florida manatee population under different scenarios regarding the presence of threats, while accounting for process variation (environmental, demographic, and catastrophic stochasticity) as well as parametric and structural uncertainty. We used the manatee core biological model (CBM) for this viability analysis, and considered the role of five threats: watercraft-related mortality, loss of warm-water habitat in winter, mortality in water-control structures, entanglement, and red tide. All scenarios were run with an underlying parallel structure that allowed a more powerful estimation of the effects of the various threats. The results reflect our understanding of manatee ecology (as captured in the structure of the CBM), our estimates of manatee demography (as described by the parameters in the model), and our characterization of the mechanisms by which the threats act on manatees. As an example of the type of results generated, we estimated that the probability of the manatee population falling to less than 250 adults on either the Atlantic or Gulf coasts (from a current statewide population size of near 3300) within 100 years is 8.6%. Complete removal of the watercraft threat alone would reduce this risk to 0.4%; complete removal of the warm-water threat to 4.2%; removal of both threats would reduce the risk to 0.1%. The modeling approach we have taken also allows us to consider partial removal of threats, as well as removal of multiple threats simultaneously. We believe the measure we have proposed (probability of quasi-extinction over y years, with quasi-extinction defined as dropping below a threshold of z on either coast) is a suitable measure of status that integrates a number of the elements that are relevant to interpretation under the ESA (it directly integrates risk of extinction and reduction of range, and indirectly integrates loss of genetic diversity). But the identification of the time frame of interest and the tolerable risk of quasi-extinction are policy decisions, and an ecology-based quasi-extinction threshold has not yet been determined. We have endeavored to provide results over a wide range of these parameters to give decision-makers useful information to assess status. This assessment of threats suggests that watercraft-related mortality is having the greatest impact on manatee population growth and resilience. Elimination of this single threat would greatly reduce the probability of quasi-extinction. Loss of warm-water is also a significant threat, particularly over the long-term. Red tide and entanglement, while noticeable threats, have had less of an impact on the manatee population. The effect of water control structures may have already been largely mitigated. We did not, however, consider an exhaustive list of threats. Other threats (e.g., reduction of food resources due to storms and development) may play a

Open-File Report↗

USGS2015

Applied Geochemistry Special Issue on Environmental geochemistry of modern mining

Environmental geochemistry is an integral part of the mine-life cycle, particularly for modern mining. The critical importance of environmental geochemistry begins with pre-mining baseline characterization and the assessment of environmental risks related to mining, continues through active mining especially in water and waste management practices, and culminates in mine closure. The enhanced significance of environmental geochemistry to modern mining has arisen from an increased knowledge of the impacts that historical and active mining can have on the environment, and from new regulations meant to guard against these impacts. New regulations are commonly motivated by advances in the scientific understanding of the environmental impacts of past mining. The impacts can be physical, chemical, and biological in nature. The physical challenges typically fall within the purview of engineers, whereas the chemical and biological challenges typically require a multidisciplinary array of expertise including geologists, geochemists, hydrologists, microbiologists, and biologists. The modern mine-permitting process throughout most of the world now requires that potential risks be assessed prior to the start of mining. The strategies for this risk assessment include a thorough characterization of pre-mining baseline conditions and the identification of risks specifically related to the manner in which the ore will be mined and processed, how water and waste products will be managed, and what the final configuration of the post-mining landscape will be. In the Fall 2010, the Society of Economic Geologists held a short course in conjunction with the annual meeting of the Geological Society of America in Denver, Colorado (USA) to examine the environmental geochemistry of modern mining. The intent was to focus on issues that are pertinent to current and future mines, as opposed to abandoned mines, which have been the focus of numerous previous short courses. The geochemical challenges of current and future mines share similarities with abandoned mines, but differences also exist. Mining and ore processing techniques have changed; the environmental footprint of waste materials has changed; environmental protection has become a more integral part of the mine planning process; and most historical mining was done with limited regard for the environment. The 17 papers in this special issue evolved from the Society of Economic Geologists’ short course. The relevant geochemical processes encompass the source, transport, and fate of contaminants related to the life cycle of a mine. Contaminants include metals and other inorganic species derived from geologic sources such as ore and solid mine waste, and substances brought to the site for ore processing, such as cyanide to leach gold. Factors, such as mine-waste mineralogy, hydrologic setting, mine-drainage chemistry, and microbial activity, that affect the hydrochemical risks from mining are reviewed by Nordstrom et al. In another paper, Nordstrom discusses baseline characterization at mine sites in a regulatory framework, and emphasizes the influence of mineral deposits in producing naturally elevated concentrations of many trace elements in surface water and groundwater. Surface water quality in mineralized watersheds is influenced by a number of processes that act on daily (diel) cycles and can produce dramatic variations in trace element concentrations as described by Gammons et al. Pre-mining baseline characterization studies should strive to capture the magnitude of these diel variations. Desbarats et al., using a case study of mine drainage from a gold mine, illustrate how elements that commonly occur as negatively charged species (anions) in solution, such as arsenic as arsenate, behave in an opposite fashion than most metals, which occur as positively charged species (cations). Significant improvement in the understanding of factors that influence the toxicity of metals to aquatic organisms in surface water has highlighted the importance of aqueous chemistry, particularly dissolved organic carbon, as described by Smith et al. Stream sediment contamination is another important pathway for affecting aquatic organisms, as reviewed by Besser et al. Understanding and predicting environmental consequences from mining begins with knowing the mineralogy and mineral reactivity of the ore, the wastes, and of secondary minerals formed later. Jamieson et al. review the importance of mineralogical studies in mine planning and remediation. A number of types of site-specific studies are needed to identify environmental risks related to individual mines. Lapakko reviews the general framework of mine waste characterization studies that are integral to the mine planning process. Hageman et al. present a comparative study of several static tests commonly used to characterize mine waste. The mining and ore processing practices employed at a specific mine site will vary on the basis of the commodities being targeted, the geology of the deposit, the geometry of the deposit, and the mining and ore processing methods used. Thus, these factors, in addition to the waste management practices used, can result in a variety of end-member mine waste features, each of which has its own set of challenges. Open pit mines and underground mines require waste rock to be removed to access ore. Waste rock presents unique problems because the rock is commonly mineralized at sub-economic grades and has not been processed to remove potentially problematic minerals, such as pyrite. Amos et al. examine the salient aspects of the geochemistry of waste rock. Mill tailings – the waste material after ore minerals have been removed – are a volumetrically important solid waste at many mine sites. Their fine grain size and the options for their management make their behavior in the environment distinct from that of waste rock. Lindsay et al. describe some of these differences through three case-study examples. Subaqueous disposal of tailings is another option described by Moncur et al. Cyanide leaching for gold extraction is a common method throughout the world. Johnson describes environmental aspects of cyanidation. Uranium mining presents unique environmental challenges, particularly since in-situ recovery has seen widespread use. Campbell et al. review the environmental geochemistry of uranium mining and current research on bioremediation. Ore concentrates from many types of metal mining undergo a pyrometallurgical technique known as smelting to extract the metal. Slag is the result of smelting, and it may be an environmental liability or a valuable byproduct, as described by Piatak et al. Finally, the open pits that result from surface mining commonly reach below the water table. At the end of mining, these pits may fill to form lakes that become part of the legacy of the mine. Castendyk et al., in two papers, review theoretical aspects of the environmental limnology of pit lakes. They also describe approaches that have been used to model pit lake water balance, wall-rock contributions to pit lake chemistry, pit lake water quality, and limnological processes, such as vertical mixing, through the use of three case studies.

Applied Geochemistry↗

USGS2025

Assessing spatial variability of nutrients, phytoplankton, and related water-quality constituents in the California Sacramento–San Joaquin Delta at the landscape scale—Comparison of four (2018, 2020, 2021, 2022) spring high-resolution mapping surveys

Executive Summary This report summarizes results from boat-based, high-resolution water-quality mapping surveys completed before, during, and after upgrades to the EchoWater Resource Recovery Facility (EchoWater Facility), the regional wastewater facility for the City of Sacramento and surrounding areas, near Elk Grove, California. Surveys were completed in the tidal aquatic environments of the Sacramento–San Joaquin Delta (Delta) in spring (May or June) 2018, 2020, 2021, and 2022. In each survey, a suite of in situ sensors were used to continuously (one measurement per second) measure water-quality conditions, nutrients, phytoplankton abundance, and species composition. In addition to in situ data collection, discrete water samples were collected about every 2 miles while underway for determination of phosphate, ammonium, and nitrate concentration. The boat stopped at about 30 locations to collect discrete samples for a suite of additional analytes, including phytoplankton enumeration. The four surveys represent snapshots in time across different phases of the EchoWater Facility Biological Nutrient Reduction (BNR) upgrade. The May 2018 survey represents conditions before the upgrade. The second survey (June 2020) represents conditions after implementation of the Nitrifying Sidestream Treatment. The third survey (May 2021) was completed immediately after the completion of the BNR upgrade and represents a transitional period, and the final survey (May 2022) represents post-upgrade conditions. Relevant hydrologic and climatic context such as water-year type, X 2 position (the distance from the Golden Gate Bridge to the point upstream where bottom salinity is 2 parts per thousand; Jassby and others, 1995), water export to import ratio, and management actions like the Delta Cross Channel gate operations are presented for each survey so they may be considered in comparisons among surveys. Differences in water-quality parameters, like turbidity, temperature, salinity, pH, and dissolved oxygen (DO) improve understanding of nutrient cycling and phytoplankton dynamics. Because the Delta is a complex system, we divided the study area into hydrologic zones to better examine general trends and obtain a broadscale view of differences among the 4 study years. Results are presented for each survey and parameter using box plots to compare the different hydrologic zones. We also present each parameter using contour maps by survey to display gradients across the system. The most evident change to water quality in the Delta across surveys is related to the EchoWater Facility BNR upgrade, which included nitrification and denitrification processes. Through this upgrade, effluent ammonium (NH 4 + ) concentrations were reduced by more than 95 percent (from about 2,000 micromolars [μM] to below the reporting limit of 35 μM), and nitrate (NO 3 − ) concentrations increased from near zero to about 500 μM; therefore, the concentration of dissolved inorganic nitrogen (DIN; the sum of NH 4 + and NO 3 − ) in the effluent was reduced by about 75 percent between May 2018 and May 2022. The BNR upgrade resulted in a reduction in NH 4 + concentrations in aquatic habitats immediately below the facility, designated as the “north Delta tidal transition zone” (Bergamaschi and others, 2024), from about 30 μM pre-upgrade to near zero during the 2022 spring survey, whereas effluent NO 3 − increased from median concentrations of about 7 μM to about 15 μM. Because of the reduced effluent nitrogen loads and variability in Sacramento River nitrogen loads from upstream sources, DIN concentrations in the north Delta tidal transition zone decreased from a median of 53.3 μM in 2018 to 35.3 μM in 2020, 20.7 μM in 2021, and 11.3 μM in 2022 during the spring surveys. The changes in DIN concentration and form observed in the north Delta tidal transition zone after the EchoWater Facility upgrade extended downstream but were rapidly altered by hydrologic mixing, biogeochemical processes, and other nutrient source inputs. Most of the Delta indicated near-zero concentrations of NH 4 + 1 year after the completion of the EchoWater Facility upgrades represented by the 2022 survey. Exceptions to this finding were observed in the San Joaquin River near Stockton and in Suisun Bay, indicating there are NH 4 + inputs to these locations from other sources (for example, Stockton Regional Wastewater Control Facility and Central Contra Costs Sanitary District wastewater treatment plants or agricultural and urban runoff). Although there was an increase in NO 3 − concentrations in the north Delta tidal transition zone after the upgrade, increases in NO 3 − in other zones were not apparent, presumably because nitrification of effluent derived ammonium was no longer a source of NO 3 − . Concentrations of DIN in many Delta zones were lower in 2022 compared to 2018 and 2020, with concentrations near or below what is considered potentially nitrogen limiting conditions for phytoplankton growth in the North Delta tidal transition zone and the Cache Slough complex channel system. Unrelated to the EchoWater Facility upgrade, NO 3 − and therefore DIN concentrations increased in the San Joaquin River near Stockton and in adjacent water bodies by survey date (likely associated with increasing drought conditions). The Mokelumne River had low DIN concentrations, except in 2018 when the Delta Cross Channel was open, which allowed nutrient-rich Sacramento River water to flow into this section of the river. Data from these surveys also support the hypothesis that nutrient drawdown during phytoplankton blooms may create localized nitrogen limiting conditions. The BNR upgrade resulted in lower effluent phosphate (PO 4 3− ) concentrations, which lowered PO 4 3− concentrations in some zones of the Delta during the four spring surveys; however, PO 4 3− concentrations throughout the Delta remained above 0.3 μM, indicating that primary productivity was not limited by phosphorous availability. DIN and PO 4 3− decreased after the upgrade in many areas of the Delta, and the DIN to dissolved inorganic phosphorus (DIN:DIP) ratio remained similar to pre-upgrade conditions and was often below the Redfield Ratio of 16, indicating nitrogen is more likely to limit phytoplankton growth than phosphorous. Inputs of dissolved organic carbon (DOC) from the EchoWater Facility are a minor source of this constituent to the Delta, so the upgrade had little to no effect on DOC concentrations across the Delta. Because phytoplankton abundance and species composition in the Delta are shaped by multiple factors other than nutrients (for example, light availability, temperature, salinity, and predation), it is important to consider these factors (as well as long-term monitoring) in addition to the EchoWater Facility upgrade. Although phytoplankton populations were low across much of the Delta during the spring surveys, several localized phytoplankton blooms (defined here as greater than 15 micrograms per liter [μg/L] of chlorophyll) provide insight into conditions that may favor the growth of beneficial and harmful species.

Callifornia↗

USGS2019

Southern sea otter (Enhydra lutris nereis) population biology at Big Sur and Monterey, California --Investigating the consequences of resource abundance and anthropogenic stressors for sea otter recovery

The range of the southern sea otter ( Enhydra lutris nereis ) spans most of the central California coast from Half Moon Bay to Gaviota. Some coastal areas within this range are heavily developed and highly impacted by humans, while other areas are wild and largely pristine. Determining the relative importance of food resource abundance, environmental conditions, and anthropogenic increases in pathogens and pollutants to population change in sea otters is critical to understanding limitations to population growth. To investigate the causal links between the sluggish population growth of sea otters in central California and factors that could be driving variation in survival and reproduction, we designed a study to compare two distinct subpopulations—one in an area of low human impact (Big Sur) and one in an area of high human impact (Monterey). Between 2008 and 2011, the U.S. Geological Survey and collaborators conducted a telemetry-based study of sea otters at these two locations. The results of this study were not consistent with the hypothesis that sea otters adjacent to human population centers (Monterey) experience higher exposure to pollutants and pathogens than those in lower impacted areas (Big Sur). In fact, based on serological analysis, female sea otters from Big Sur showed higher exposure rates to Toxoplasma gondii than did female otters from Monterey, while domoic acid exposure appeared to be similar at both sites. Gene expression (specifically transcription) analysis did not indicate any consistent differences between the two populations that would have suggested a response to pathogen or toxin exposure, although there were temporal changes in gene transcription for sea otters at Big Sur following potential exposure to run-off from wildfires that occurred during the study. Together, these metrics suggest that variation in exposure to environmental stressors occurred, but patterns were not clearly attributable to differences in human population densities or land-use patterns. When compared to Monterey, sea otters in Big Sur spent more time feeding, had a higher degree of dietary specialization, were in poorer body condition, and had lower survival rates (both pups and adults). Together, these metrics suggest that otters at Big Sur had greater nutritional stress, consistent with lower per-capita resource abundance. Overall, study results indicate that density-dependent population regulation, mediated by per-capita resource abundance, is the most significant factor currently limiting population growth in the center part of the range. Additionally, spatial and temporal variation in environmental and anthropogenic stressors also can affect sea otter health, although patterns of variation are complex and are not simply a function of proximity to human populations. We also found that exposure to environmental stressors (either natural or anthropogenic in origin) often is associated with resource limitation. Finally, our results indicate that sea otter populations are structured at relatively small spatial scales, and the processes that regulate population abundance (including density-dependent resource abundance) also occur at these smaller, more local scales.

California↗

USGS2011

Summary report of responses of key resources to the 2000 Low Steady Summer Flow experiment, along the Colorado River downstream from Glen Canyon Dam, Arizona

In the spring and summer of 2000, a series of steady discharges of water from Glen Canyon Dam on the Colorado River were used to evaluate the effects of aquatic habitat stability and water temperatures on native fish growth and survival, with a special focus on the endangered humpback chub (Gila cypha), downstream from the dam in Grand Canyon. The steady releases were bracketed by peak powerplant releases in late-May and early-September. The duration and volume of releases from the dam varied between spring and summer. The intent of the experimental hydrograph was to mimic predam river discharge patterns by including a high, steady discharge in the spring and a low, steady discharge in the summer. The hydrologic experiment was called the Low Steady Summer Flow (LSSF) experiment because steady discharges of 226 m3/s dominated the hydrograph for 4 months from June through September 2000. The experimental hydrograph was developed in response to one of the U.S. Fish and Wildlife Service's Recommended and Prudent Alternatives (RPA) in its Biological Opinion of the Operation of Glen Canyon Dam Final Environmental Impact Statement. The RPA focused on the hypothesis that seasonally adjusted steady flows were dam operations that might benefit humpback chub more than the Record of Decision operations, known as Modified Low Fluctuating Flow (MLFF) operations. Condensed timelines between planning and implementation (2 months) of the experiment and the time required for logistics, purchasing, and contracting resulted in limited data collection during the high-release part of the experiment that occurred in spring. The LSSF experiment is the longest planned hydrograph that departed from the MLFF operations since Record of Decision operations began in 1996. As part of the experiment, several studies focused on the responses of physical properties related to environments that young-of-year (YOY) native fish might occupy (for example, measuring mainstem and shoreline water temperature, and quantifying useable shorelines). The part of the hydrograph that included a habitat maintenance flow (a 4-day spike at a powerplant capacity of 877 m3/s) and sustained high releases in April and May (averaging 509 m3/s) resulted in sediment export to Lake Mead, the reservoir downstream from Glen Canyon Dam, which is outside the study area. Some mid-elevation sandbar building (between 566 and 877 m3/s stage elevations) occurred from existing sediment deposits rather than from sediment inputs from tributaries during the previous winter. Low releases in the summer combined with low tributary sediment inputs resulted in minor sediment accumulation in the study area. The September habitat maintenance flow reworked accumulated sediment and resulted in increases in the area of some backwaters. The mainstem water temperatures in the reach near the Little Colorado River during the LSSF experiment varied little from previous years. Mainstem water temperatures in western Grand Canyon average 17 to 20 degrees C. During the LSSF, backwaters warmed more than other shoreline environments during the day, but most backwaters returned to mainstem water temperatures overnight. Shoreline surface water temperatures from river mile (RM) 30 to 72 varied between 9 and 28 degrees C in the middle of the day in July. These temperatures are within the optimal temperature range for humpback chub growth and spawning, which is between 15 and 24 degrees C. How surface water temperatures transfer to subsurface water temperatures is unknown. Data collection associated with the response of fish to the 2000 LSSF hydrograph focused on fish growth and abundance along the Colorado River in Grand Canyon. The target resource, humpback chub and other native fishes, did not respond in a strongly positive or strongly negative manner to the LSSF hydrograph during the sampling period, which extended from June to September 2000. In 2000, the mean total length of YOY native fishes was similar to the mean

Arizona↗

USGS2010

The potential influence of changing climate on the persistence of salmonids of the inland west

The Earth's climate warmed steadily during the 20th century, and mean annual air temperatures are estimated to have increased by 0.6°C (Intergovernmental Panel on Climate Change, 2007). Although many cycles of warming and cooling have occurred in the past, the most recent warming period is unique in its rate and magnitude of change (Siegenthaler and others, 2005) and in its association with anthropogenic emissions of greenhouse gases (Intergovernmental Panel on Climate Change , 2007). The climate in the western United States warmed in concert with the global trend but at an accelerated rate (+0.8°C during the 20th century; Saunders and others, 2008). The region could also prove especially sensitive to future changes because the relatively small human population is growing rapidly, as are demands on limited water supplies. Regional hydrological patterns are dominated by seasonal snow accumulation at upper elevations. Most of the region is relatively dry, and both terrestrial and aquatic ecosystems are strongly constrained b y water availability (Barnett and others, 2008; Brown and others, 2008). Stream environments are dynamic and climatically extreme, and salmonid fishes are the dominant elements of the native biodiversity (McPhail and Lindsey, 1986; Waples and others, 2008). Salmonids have broad economic and ecologic importance, but a century of intensive water resource development, nonnative fish stocking, and land use has significantly reduced many populations and several taxa are now protected under the Endangered Species Act (Thurow and others, 1997; Trotter, 2008). Because salmonids require relatively pristine, cold water environments and are often isolated in headwater habitats, members of this group may be especially vulnerable to the effects of a warming climate (Keleher and Rahel, 1996; Rieman and others, 2007; Williams and others, 2009). Warming during the 20th century drove a series of environmental trends that have profound implications for many aspects of salmonid habitat, including disturbance regimes such as wildfire, and unfavorable changes to thermal and hydrologic properties of aquatic systems. Warmer air temperatures have been associated with decreased winter snow accumulations, have accelerated snowmelt, and have advanced the timing of peak runoff by several days to weeks across most of western North America (Stewart and others, 2005; Barnett and others, 2008). Less snow and earlier runoff decrease aquifer recharge, make less water available for groundwater inputs to streams, and are contributing to widespread decreases in summer low flows (Stewart and others, 2005; Rood and others, 2008; Luce and Holden 2009). Interannual variability in stream flow is increasing, as is the persistence of multi-year extreme conditions (McCabe and others, 2004; Pagano and Garen 2005). In many areas of western North America, flood risks have increased in association with warmer temperatures during the 20th century (Hamlet and Lettenmaier, 2005). Streams where midwinter temperatures are near freezing have proven especially sensitive to increased flooding because of associated transitional hydrological patterns (mixtures of rainfall and snowmelt) and propensity for occasional rain-on-snow events to rapidly melt winter snowpack and generate large floods (Hamlet and Lettenmaier, 2005). Stream temperatures in many areas are increasing (Peterson and Kitchell, 2001; Morrison and others, 2002; Bartholow, 2005; Kaushal and others, 2010), due to both air temperature increases and reduced summer flows that make streams more sensitive to warmer air temperatures (Isaak and others, 2010). In recent decades, wildfires have become more common across much of the western United States during periods of more frequent droughts (Westerling and others, 2006; Hoerling and Eischeid, 2007), and local stream temperature can increase in postfire environments (Gresswell, 1999; Dunham and others, 2007). Fire-related temperature increase within streams is commonly a transient phenomenon, lasting only until riparian vegetation has recovered (Gresswell, 1999); however, ongoing climate change could preclude recovery to higher stature, prefire vegetation types in some areas (McKenzie and others, 2004; van Mantgem and Stephenson, 2007), resulting in a loss of critical riparian shading. Additionally, when wildfires occur in steep mountain topographies, the vegetation that stabilize s soils on hillslopes is often killed and landslides become more prevalent (Gresswell, 1999). Landslides int o stream channels form debris flows composed of sediment slurries and dead trees that can scour channels to bedrock and further exacerbate stream heating, delay recovery of riparian areas, or extirpate fish populations (Gresswell, 1999; May and Gresswell, 2003; Dunham and others, 2007). Changes in stream environments will shift habitat distributions, sometimes unpredictably, in both time and space for many salmonid fishes. Water temperature fundamentally influences aquatic ecosystem health because distribution, reproduction, fitness, and survival of ectothermic organisms are inextricably linked to the thermal regime of the environment. Historically, research has focused on defining lethal thermal limits of salmonids (Eaton and others, 1995; Selong and others, 2001; Todd and others, 2008); however, water temperature is known to be important in biological processes at a variety of spatial scales and levels of biological organization (Rahel and Olden, 2008; McCullough and others, 2009). For instance, trout are affected directly by water temperature through feeding, metabolism, and growth rates, and indirectly by factors such as prey availability and species interactions (Wehrly and others, 2007; Rahel and Olden, 2008). Where cold water temperatures currently limit habitat suitability and distributions of some species (for example, at the highest and most northerly distributional extents; Nakano and others, 1996; Coleman and Fausch, 2007), a warming climate may gradually increase the quality and extent of suitable habitat. Over time, previously constrained populations are expected to expand into these new habitats and increase in number. Some evidence suggests this may already be happening in Alaska, where streams in recently deglaciated areas are being colonized by emigrants from nearby salmon and char populations (Milner and others, 2000). Unfortunately, many of the sensitive salmonid species that are often the focus of western managers are unlikely to benefit from future water temperature increases. Warmer stream temperatures will facilitate invasion by nonnative species that are broadly established in downstream areas into upstream areas where they will compete with native species (Rieman and others, 2006; Rahel and Olden, 2008; Fausch and others, 2009). In other cases, warmer stream temperatures will render thermally suitable habitats unsuitable in downstream areas and effect net losses of habitat because upstream distributions are often constrained by streams that are too small or steep (Hari and others, 2006; Isaak and others, 2010). Both scenarios are realistic for fish species like bull trout ( Salvelinus confluentus ) (Rieman and others, 2006; Rieman and others, 2007), the various subspecies of cutthroat trout ( Oncorhynchus clarkii ) (Williams and others, 2009), Gila trout ( Oncorhynchus gilae gilae ) (Kennedy and others, 2008), and Apache trout ( Oncorhynchus gilae apache ) (Rinne and Minckley, 1985; Carmichael and others, 1993). As native species are increasingly confined to smaller and more isolated habitats by a gradually warming climate, the effects of wildfires (whether related to lethal changes in water quality during a fire, channel debris flows, or chronic postfire warming ) could have greater proportional effects on remaining habitats (for example, Brown and others, 2001; Rieman and others, 2007). If these changes were accompanied by additional hydrologic alterations associated with changes to the magnitude, frequency, duration, timing, and rate of change of discharge patterns (Jager and others, 1999; Henderson and others, 2000), populations may begin to lose some of their historic resilience and become ever more susceptible to local extirpations. As dramatic and extensive as climatic and environmental trends are for salmonid habitats, global climate models (GCMs) project that many of these trends will continue and even accelerate until at least the middle of the 21st century (Intergovernmental Panel on Climate Change, 2007). Current projections suggest mean annual air temperatures will increase by an additional 1–3°C, and early indications are that climate trajectory is at the higher end of this range (Pittock, 2006; Raupach and others, 2007). Although predicted changes vary considerably, even the most conservative estimates suggest a warming rate that will be twice that observed during the 20th century. Projections for the midcentury are most certainly due to the effects of greenhouse gases already emitted or predicted in the short term, uncertainties of the effects of longer-term greenhouse gas emissions, short-term climate cycles, and process errors associated with climate models (Cox and Stephenson, 2007). Projections of changes in total precipitation are less certain than those for air temperatures, but most GCMs project relatively small changes in the Northwest, with the exception of slightly drier summer periods (Mote and others, 2008; Karl and others, 2009). In the Southwest, however, significant decreases (such as 15–30 percent ) are projected during most periods of the year, and this area is one of the few for which Intergovernmental Panel on Climate Change (2007) precipitation projections have a high level of certainty (Hoerling and Eischeid, 2007; Karl and others, 2009). Clearly, managers of native salmonids in the wester n United States should consider adjusting management strategies to accommodate a warmer and possibly drier future (Williams and others, 2009). Tools are needed to forecast where important changes may occur and how conservation efforts should be prioritized. In this Open-File Report, we document our initial efforts in this regard for 10 species and subspecies of inland trout and Montana Arctic grayling ( Thymallus arcticus ) across the western United States.

Arizona, California, Colorado, Idaho, Montana, Nev↗

USGS2013

Preliminary assessment of bioengineered fringing shoreline reefs in Grand Isle and Breton Sound, Louisiana

Restoration of three-dimensional shell habitats in coastal Louisiana presents a valuable and potentially self-sustaining approach to providing shoreline protection and critical nekton habitat and may contribute to water quality maintenance. The use of what has been called “living shorelines” is particularly promising because in addition to the hypothesized shoreline protection services, it is predicted that, if built and located in viable sites, these living shorelines may ultimately contribute to water quality maintenance through filtration of bivalves and may enhance nekton habitat. This approach, however, has not been tested extensively in different shallow water estuarine settings; understanding under what conditions a living shoreline must have to support a sustainable oyster population, and where these reefs may provide valuable shoreline protection, is key to ensuring that this approach provides an effective tool for coastal restoration. This project gathered preliminary data on the sustainability and shoreline stabilization of three large bioengineered fringing reefs located in Grand Isle, Lake Eloi, and Lake Fortuna, Louisiana. We collected preconstruction and postconstruction physiochemical and biological data by using a before-after-control-impact approach to evaluate the effectiveness of these living shoreline structures on reducing marsh erosion, enabling reef sustainability, and providing other ecosystem benefits. Although this project was originally designed to compare reef performance and impacts across three different locations over 2 years, delays in construction because of the Deepwater Horizon oil spill resulted in reefs being built from 12 to 18 months later than anticipated. As a result, monitoring postconstruction was severely limited. One reef, Grand Isle, was completed in March 2011 and monitored up to 18 months postcreation, whereas Lake Eloi and Lake Fortuna reefs were not completed until January 2012, and only 8 months of postconstruction data are available. Data for the latter two sites thus reflect only the 2012 spring/summer seasons, which were further impacted by a direct hit by Hurricane Isaac in August 2012, which resulted in shoreward movement of approximately 14 percent of the bioengineered structures at Lake Fortuna. Given the shortened monitoring timeframe and significant differences in construction schedules, we were not able to provide a full postconstruction assessment of the sites or a full comparison of site success based on local site characteristics. Because many of the impacts that were identified for monitoring reflect long-term processes, results and data presented should be interpreted cautiously. Sustainable oyster reefs require recruitment, growth, and survival at a rate that keeps pace with mortality and shell disarticulation. Although one site failed to recruit (establishment plus survival > 50 millimeters [mm]) over two spawning seasons, two sites only had 6 months postconstruction data available for assessment. Although there are good data on the requirements for oyster growth, there is limited explicit information on the site-specific water quality, hydrodynamic, and biological interaction effects that may determine successful reef establishment. Furthermore, interannual variability can significantly affect reef establishment, and our shortened timeframe of sampling (less than one spawning season for two of the reefs; two spawning seasons for one reef), combined with a lack of prerestoration monitoring data, limit our ability to draw any conclusions about long-term reef sustainability. Bioengineered reefs are thought to provide some benefits to shoreline stabilization through their structure by immediately attenuating wave energies and directly reducing erosion rates at shorelines sheltered by the reefs but also by increasing sediment deposition behind the reefs. Preliminary data indicate differences in reef impact by site; given the short timeframe of postconstruction data at two of the sites, and differences in reef placement between sites, however, it is difficult to draw any conclusions. Longer-term data collection and further analyses comparing reef placement; local wind, wave energy, sediment transport processes; and local bathymetry may help in parameterizing sites where fringing reefs may be most beneficial for shoreline protection. In addition to basic reef sustainability and shoreline stabilization, we measured both water quality parameters and nekton abundances around the newly created reefs and adjacent reference sites. Within the timeframe of monitoring, no effect of reefs on water quality was detected at any site. Given that water quality effects are hypothesized to result from the filtration activities of bivalves, and reefs either failed to recruit (settlement plus survival to > 50 mm) or successfully recruited but only had a couple months of growth prior to this report, it was not expected that an effect would be detectable in this timeframe. Nekton such as blue crab, gulf menhaden, and anchovies were found to be more abundant on the reefs; larger, more transient species were not found to be affected by reef presence. Future work examining smaller organisms and juveniles, including more explicit studies examining why and how these organisms preferentially use oyster reefs, would be useful in the design of other bioengineered reefs and help in understanding the role of the reefs in supporting the nekton community. It is clear from the initial work that ensuring correct site selection by better understanding what local site factors influence oyster populations is key to establishing successful living shoreline reefs. Ultimately, the success of the reefs in providing any ecosystem service relies on their ability to build a viable oyster population that is self-sustaining over the long term. As many of the ecosystem processes hypothesized to result from reefs develop over the long term (4–6 years), some level of monitoring over the next few years is highly recommended in order to accurately assess the long term viability of the reefs, their provision of ecosystem services, and to provide better guidance for future projects.

Louisiana↗

USGS2023

Near-field receiving-water monitoring of trace metals and a benthic community near the Palo Alto Regional Water Quality Control Plant in south San Francisco Bay, California—2020

Trace-metal concentrations in sediment and in the clam Limecola petalum (World Register of Marine Species, 2020; formerly reported as Macoma balthica and M. petalum ), clam reproductive activity, and benthic macroinvertebrate community structure were investigated in a mudflat 1 kilometer (km) south of the discharge of the Palo Alto Regional Water Quality Control Plant (PARWQCP) in south San Francisco Bay, California. This report includes the data collected by the U.S. Geological Survey (USGS) for January 2020–December 2020 (Cain and others, 2022). These data append to long-term datasets extending back to 1974. A major focus of the report is an integrated description of the 2020 data within the context of the longer, multidecadal dataset. This dataset supports the City of Palo Alto’s Near-Field Receiving- Water Monitoring Program, initiated in 1994. Silver and copper contamination substantially decreased at the site in the 1980s following the implementation by PARWQCP of advanced wastewater-treatment and source-control measures. Since the 1990s, concentrations of these elements in surface sediments have continued to decrease, although more slowly. For example, from 1994 to 2020, the minimum annual mean silver concentration—0.20 milligram per kilogram (mg/kg)—was observed in multiple years. In 2020, silver concentrations ranged from 0.18 to 0.28 mg/kg. These concentrations are 2 to 3 times higher than the regional background concentration. Presently (2020), sediment-copper concentrations appear to be near the regional background level. Over the same period (1994–2020), sedimentary iron and zinc exhibited modest decreases. Sedimentary aluminum, chromium, mercury, nickel, and selenium have not exhibited any trend. Since 1994, silver and copper concentrations in L. petalum have varied seasonally, apparently in response to a combination of site-specific metal exposures and cyclic growth and reproduction, as reported previously. Seasonal patterns for other elements, including chromium, mercury, nickel, selenium, and zinc, generally were similar in timing and magnitude as those for silver and copper. Downward trends in the silver and zinc concentrations in L. petalum during 1994–2020 were evident and appeared to be related to the general physiological condition of the clam, indicated by a condition index. Biological effects of elevated silver and copper contamination at the Palo Alto site have been interpreted from data collected during and after the recession of these contaminants. Concentrations of both elements in the soft tissues of L. petalum decreased with sedimentary copper and silver. This pattern was associated with changes in the reproductive activity of L. petalum , as well as the structure of the benthic invertebrate community. Reproductive activity of L. petalum increased as metal concentrations in L. petalum decreased (Hornberger and others, 2000), and presently is stable with almost all animals initiating reproduction in the fall and spawning the following spring. Analyses of the benthic community structure indicate that the infaunal invertebrate community has shifted from one dominated by several opportunistic species when silver and copper exposures were highest to one in which the species abundance is more evenly distributed, a pattern that indicates a more stable community that is subjected to fewer stressors. Importantly, this long-term change is unrelated to other metals and other measured environmental factors, including salinity and sediment composition. In addition, two of the opportunistic species ( Ampelisca abdita and Streblospio benedicti ) that brood their young and live on the surface of the sediment in tubes have shown a continual decrease in dominance coincident with the decrease in metals. Both species had short-lived rebounds in abundance in 2008, 2009, and 2010 and showed signs of increasing abundance in 2020. Heteromastus filiformis (a subsurface polychaete worm that lives in the sediment, consumes sediment and organic particles residing in the sediment, and reproduces by laying its eggs on or in the sediment) showed a concurrent increase in dominance and, in the last several years before 2008, showed a stable population. H. filiformis abundance increased slightly from 2011 to 2012 and returned to pre-2011 numbers in 2020. The reproductive mode of most species that were present in 2020 was indicative of species that were capable of movement either as pelagic larvae or as mobile adults. Although oviparous species were lower in number in this group, the authors hypothesize that these species will return slowly as more species move back into the area. The use of functional ecology was highlighted in the 2020 benthic community data, which showed that the animals that have now returned to the mudflat are those that can respond successfully to a physical, nontoxic disturbance. Today, community data show a mix of species that consume the sediment, or filter feed, those that have pelagic larvae that must survive landing on the sediment, and those that brood their young. The long-term recovery observed after the 1970s can be ascribed to the decrease in sediment pollutants.

California↗

USGS2014

Conservation buffer distance estimates for Greater Sage-Grouse: a review

This report was prepared at the request of the U.S. Department of the Interior and is a compilation and summary of published scientific studies that evaluate the influence of anthropogenic activities and infrastructure on Greater Sage-Grouse (Centrocercus urophasianus ; hereafter, sage-grouse) populations. The purpose of this report is to provide a convenient reference for land managers and others who are working to develop biologically relevant and socioeconomically practical buffer distances around sage-grouse habitats. The framework for this summary includes (1) addressing the potential effects of anthropogenic land use and disturbances on sage-grouse populations, (2) providing ecologically based interpretations of evidence from the scientific literature, and (3) informing implementation of conservation buffers around sage-grouse communal breeding locations—known as leks. We do not make specific management recommendations but instead provide summarized information, citations, and interpretation of findings available in scientific literature. We also recognize that because of variation in populations, habitats, development patterns, social context, and other factors, for a particular disturbance type, there is no single distance that is an appropriate buffer for all populations and habitats across the sage-grouse range. Thus, we report values for distances upon which protective, conservation buffers might be based, in conjunction with other considerations. We present this information for six categories of land use or disturbance typically found in land-use plans which are representative of the level of definition available in the scientific literature: surface disturbance (multiple causes; immediate and cumulative influences); linear features (roads); energy development (oil, gas, wind, and solar); tall structures (electrical, communication, and meteorological); low structures (fences and buildings); and activities (noise and related disruptions). Minimum and maximum distances for observed effects found in the scientific literature, as well as a distance range for possible conservation buffers based on interpretation of multiple sources, expert knowledge of the authors regarding affected areas, and the distribution of birds around leks are provided for each of the six categories These interpreted values for buffer distances are an attempt to balance the extent of protected areas with multiple land-use requirements using estimates of the distribution of sage-grouse habitat. Conservation efforts may then focus on the overlap between potential effect zone and important habitats. We provide a brief discussion of some of the most relevant literature for each category. References associated with the minimum and maximum values are identified in the References Cited section with corresponding symbols. Distances in this report reflect radii around lek locations because these locations are typically (although not universally) known, and management plans often refer to these locations. Lek sites are most representative of breeding habitats, but their locations are focal points within populations, and as such, protective buffers around lek sites can offer a useful solution for identifying and conserving seasonal habitats required by sage-grouse throughout their life cycle. However, knowledge of local and regional patterns of seasonal habitat use may improve conservation of those important areas, especially regarding the distribution and utilization of nonbreeding season habitats (which may be underrepresented in lek-based designations).

Open-File Report↗

USGS1998

Concepts for monitoring water quality in the Spokane River Basin, northern Idaho and eastern Washington

Numerous environmental studies have been conducted in the Spokane River Basin over the past several decades by government agencies, academic institutions, and environmental engineering firms. Most of these efforts have focused on the environmental effects of more than a century of silver, lead, and zinc mining and oreprocessing activities in the South Fork Coeur d'Alene River valley in northern Idaho. Several studies also have assessed the water quality and potential for eutrophication of Coeur d'Alene and Long Lakes and the Coeur d'Alene, St. Joe, and Spokane Rivers. Because past investigations often were limited in scope and employed different approaches and methods, an integrated understanding of hydrologic, water-quality, and aquatic biological conditions still is lacking for the basin as a whole. Substantial resources are being spent for water-quality and naturalresource management, and for mitigating the adverse environmental effects of past mining activities in the basin. A water-quality monitoring network, integrated with the decision-making processes associated with these efforts, could be of considerable value. The purpose of such a monitoring network is to produce high-quality information on which to base sound water-quality and natural-resource management decisions and to assess the effectiveness of those decisions. A streamflow- and water-quality monitoring infrastructure already exists in the Spokane River Basin. This infrastructure consists of 20 lake-stage and streamflow-gaging stations, representing specific drainages or subdrainages and, in many cases, specific stream reaches or subreaches. These gaging stations are operated by the U.S. Geological Survey (USGS), several of them in cooperation with State and Federal agencies and a private utility company. Extensive streamflow data are available, some dating from the late 1800s. Water-quality data are also available from recent USGS cooperative studies in the Coeur d'Alene Lake watershed. A nutrient load/lake response (eutrophication) model has been developed for Coeur d'Alene Lake. Hydraulic models for estimating streamflow through the low-gradient reaches of the Coeur d'Alene and St. Joe Rivers have been developed. Trace-element concentrations and distributions in sediments in the lower South Fork and main-stem Coeur d'Alene River flood plain and the bed of Coeur d'Alene Lake have been assessed. Trace-element transport models have been developed for the lower Coeur d'Alene River system; estimates of annual load are available from the early 1990's to the present (1998). The USGS is monitoring traceelement concentrations and transport at seven gaging stations in the lower Coeur d'Alene River system and upper Spokane River, in cooperation with the U.S. Environmental Protection Agency. Fish and macroinvertebrate community assessment and tissue contaminant analyses at four Coeur d'Alene and St. Joe River gaging stations will begin in 1998, either as part of the Idaho Surface- Water Quality Ambient Monitoring Network operated by USGS in cooperation with the Idaho Division of Environmental Quality, or for the Northern Rockies Intermontane Basins (NROK) study of the USGS National Water-Quality Assessment (NAWQA) Program. Several gaging stations in the Spokane River Basin are being considered for routine sampling sites for the NROK NAWQA study. Several other sites also will be sampled for contaminants in bed sediment and fish tissue for the NROK study. Combined with appropriate sampling and data interpretation strategies, the existing USGS gaging-station network and data base could provide integrated water-quality information needed for sound environmental and resource-management decisions throughout the Spokane River Basin.

Idaho;Washington↗

USGS2025

Environmental characteristics of select managed ponds in the Sacramento–San Joaquin Delta—Implications for native fish conservation and research

The use of wetlands to support native fish research and conservation efforts in the Sacramento–San Joaquin Delta (Delta) of California is a growing priority. The purpose of our study was to examine the physiochemical and biological characteristics of select managed ponds in the Delta to determine if they would be suitable habitats for research involving the conservation of delta smelt ( Hypomesus transpacificus ). We studied 10 managed ponds distributed across the central part of the Delta situated on Bacon Island and Bouldin Island in San Joaquin County, and Holland Tract and Webb Tract islands in Contra Costa County. The managed ponds had a diversity of physical habitat configurations and were not directly connected to waterways surrounding the islands and, therefore, not affected by tides. We studied the managed ponds from approximately November 2021 to December 2023 to assess water quality, zooplankton, fish, and pesticide metrics. Water levels in the managed ponds were managed to varying degrees and were mostly independent of climate-driven wet-dry seasonality. Water quality conditions varied among ponds and were independent of geographic location. Overall, mean monthly chlorophyll a concentration ranged from 15 to 57 (mean=30) micrograms per liter (μg/L), dissolved oxygen concentration ranged from 4 to 9 (mean=7) milligrams per liter (mg/L), pH was 8, salinity was 1 practical salinity units (PSU), specific conductance ranged from 1,202 to 1,839 (mean=1,471) microsiemens per centimeter (μS/cm), and turbidity ranged from 13 to 24 (mean=19) Formazin Nephelometric Units (FNU). Water temperature thresholds that contribute to stress (21 degrees Celsius [°C]) and mortality (28 °C) of delta smelt were often exceeded during summer and fall, though vertical stratification contributed to lower bottom temperatures in the deepest managed ponds, which could potentially provide thermal refugia for delta smelt so long as dissolved oxygen concentrations are suitable. Zooplankton populations were broadly similar among managed ponds and included calanoid and cyclopoid copepods that would be suitable prey for delta smelt. Overall average total zooplankton biomass, as measured with a Schindler-Patalas trap, was 0.6 μg/L (min=0, max=63.6) and peaked during spring at more than 4 μg/L. Fish populations highly varied among the managed ponds with potential predators of delta smelt such as largemouth bass ( Micropterus salmoides ) and black crappie ( Pomoxis nigromaculatus ) present in several of the managed ponds; predator distribution among ponds seemed to have been driven primarily by deliberate stocking to facilitate local fisheries. Measured pesticide concentrations were below U.S. Environmental Protection Agency Aquatic Life Benchmarks except for exceedances of three compounds (diuron [herbicide], clothianidin [insecticide], and deltamethrin [pyrethroid insecticide]) in samples collected from ponds on Bouldin Island and Webb Tract. Overall, most managed ponds seemed suitable to support delta smelt, though physical control of potential predators and summer temperature might be needed. The results provide guidance on how to engineer and manage new managed ponds to support research and conservation efforts for delta smelt and other native fishes.

California↗

USGS2017

An expert elicitation process to project the frequency and magnitude of Florida manatee mortality events caused by red tide (Karenia brevis)

Red tides (blooms of the harmful alga Karenia brevis ) are one of the major sources of mortality for the Florida manatee ( Trichechus manatus latirostris ), especially in southwest Florida. It has been hypothesized that the frequency and severity of red tides may increase in the future because of global climate change and other factors. To improve our ecological forecast for the effects of red tides on manatee population dynamics and long-term persistence, we conducted a formal expert judgment process to estimate probability distributions for the frequency and relative magnitude of red-tide-related manatee mortality (RTMM) events over a 100-year time horizon in three of the four regions recognized as manatee management units in Florida. This information was used to update a population viability analysis for the Florida manatee (the Core Biological Model). We convened a panel of 12 experts in manatee biology or red-tide ecology; the panel met to frame, conduct, and discuss the elicitation. Each expert provided a best estimate and plausible low and high values (bounding a confidence level of 80 percent) for each parameter in each of three regions (Northwest, Southwest, and Atlantic) of the subspecies’ range (excluding the Upper St. Johns River region) for two time periods (0−40 and 41−100 years from present). We fitted probability distributions for each parameter, time period, and expert by using these three elicited values. We aggregated the parameter estimates elicited from individual experts and fitted a parametric distribution to the aggregated results. Across regions, the experts expected the future frequency of RTMM events to be higher than historical levels, which is consistent with the hypothesis that global climate change (among other factors) may increase the frequency of red-tide blooms. The experts articulated considerable uncertainty, however, about the future frequency of RTMM events. The historical frequency of moderate and intense RTMM (combined) in the Southwest region was 0.35 (80-percent confidence interval [CI]: 0.21−0.52), whereas the forecast probability was 0.48 (80-percent CI: 0.30−0.64) over a 40-year projected time horizon. Moderate and intense RTMM events are expected to continue to be most frequent in the Southwest region, to increase in mean frequency in the Northwest region (historical frequency of moderate and intense RTMM events [combined] in the Northwest region was 0, whereas the forecast probability was 0.12 [80-percent CI: 0.02−0.39] over a 40-year projected time horizon) and in the Atlantic region (historical frequency of moderate and intense RTMM events [combined] in the Atlantic region was 0.05 [80-percent CI: 0.005–0.18], whereas the forecast probability was 0.11 [80-percent CI: 0.03−0.25] over a 40-year projected time horizon), and to remain absent from the Upper St. Johns River region. The impact of red-tide blooms on manatee mortality has been measured for the Southwest region but not for the Northwest and Atlantic regions, where such events have been rare. The expert panel predicted that the median magnitude of RTMM events in the Atlantic and Northwest regions will be much smaller than that in the Southwest; given the large uncertainties, however, they acknowledged the possibility that these events could be larger in their mortality impacts than in the Southwest region. By its nature, forecasting requires expert judgment because it is impossible to have empirical evidence about the future. The large uncertainties in parameter estimates over a 100-year timeframe are to be expected and may also indicate that the training provided to panelists successfully minimized one common pitfall of expert judgment, that of overconfidence. This study has provided useful and needed inputs to the Florida manatee population viability analysis associated with an important and recurrent source of mortality from harmful algal blooms.

Open-File Report↗

USGS1998

Natural attenuation of chlorinated-hydrocarbon contamination at Fort Wainwright, Alaska: A hydrogeochemical and microbiological investigation workplan

Natural attenuation processes include biological degradation, by which microorganisms break down contaminants into simpler product compounds; adsorption of contaminants to soil particles, which decreases the mass of contaminants dissolved in ground water; and dispersion, which decreases dissolved contaminant concentrations through dilution. The primary objectives of this study are to (1) assess the degree to which such natural processes are attenuating chlorinated-hydrocarbon contamination in ground water, and (2) evaluate the effects of ground-water/surface-water interactions on natural-attenuation processes in the area of the former East and West Quartermasters Fueling Systems for Fort Wainwright, Alaska. The study will include investigations of the hydrologic, geochemical, and microbiological processes occurring at this site that influence the transport and fate of chlorinated hydrocarbons in ground water. To accomplish these objectives, a data-collection program has been initiated that includes measurements of water-table elevations and the stage of the Chena River; measurements of vertical temperature profiles within the subsurface; characterization of moisture distribution and movement in the unsaturated zone; collection of ground-water samples for determination of both organic and inorganic chemical constituents; and collection of ground-water samples for enumeration of microorganisms and determination of their potential to mineralize contaminants. We will use results from the data-collection program described above to refine our conceptual model of hydrology and contaminant attenuation at this site. Measurements of water-table elevations and river stage will help us to understand the magnitude and direction of ground-water flow and how changes in the stage of the Chena River affect ground-water flow. Because ambient ground water and surface water typically have different temperature characteristics, temperature monitoring will likely provide further insight into ground-water/surface-water interactions in the subsurface. Characterization of the unsaturated zone will improve our understanding of interactions among ground water, the unsaturated zone, and the atmosphere. The interactions likely of importance to this study include the migration of water, dissolved contaminants, nutrients, and gases (oxygen, carbon dioxide, and methane) between the saturated and unsaturated zones. We will use the results of ground-water chemical analyses to determine the spatial and temporal distribution of (1) chlorinated-hydrocarbon contaminants and their degradation products, (2) oxidation-reduction indicators, (3) nutrients, and (4) major ground-water ions. These water-quality data will provide insight into ground-water flow directions, interactions between ground water and surface water, attenuation of contaminant concentrations caused by dispersion, and intrinsic microbiological processes. Microbiological analyses will indicate whether microorganisms at the site are capable of degrading the contaminants of interest, and will allow us to estimate their potential to attenuate existing contamination. Physical and chemical data interpreted as part of the analysis of ground water and surface water mixing will improve our understanding of the relationship between water quality and contaminant source mixing.

Alaska↗

USGS2009

Coastal Circulation and Sediment Dynamics in War-in-the-Pacific National Historical Park, Guam; measurements of waves, currents, temperature, salinity, and turbidity, June 2007-January 2008

Flow in and around coral reefs affects a number of physical, chemical and biologic processes that influence the health and sustainability of coral reef ecosystems. These range from the residence time of sediment and contaminants to nutrient uptake and larval retention and dispersal. As currents approach a coast they diverge to flow around reef structures, causing high horizontal and vertical shear. This can result in either the rapid advection of material in localized jets, or the retention of material in eddies that form in the lee of bathymetric features. The high complexity and diversity both within and between reefs, in conjunction with past technical restrictions, has limited our understanding of the nature of flow and the resulting flux of physical, chemical, and biologic material in these fragile ecosystems. Sediment, nutrients, and other pollutants from a variety of land-based activities adversely impact many coral reef ecosystems in the U.S. and around the world. These pollutants are transported in surface water runoff, groundwater seepage, and atmospheric fallout into coastal waters, and there is compelling evidence that the sources have increased globally as a result of human-induced changes to watersheds. In Guam, and elsewhere on U.S. high islands in the Pacific and Caribbean, significant changes in the drainage basins due to agriculture, feral grazing, fires, and urbanization have in turn altered the character and volume of land-based pollution released to coral reefs. Terrigenous sediment run-off (and the associated nutrients and contaminants often absorbed to it) and deposition on coral reefs are recognized to potentially have significant impact on coral health by blocking light and inhibiting photosynthesis, directly smothering and abrading coral, and triggering increases in macro algae. Studies that combine information on watershed, surface water- and groundwater-flow, transport and fate of sediment and other pollutants in the reef environment, and their impact on reef health and ecology are essential for effective reef management. Two of the main anthropogenic activities along west-central Guam's coastline that may impact the region's coral reef ecosystems include pollution and coastal land use/development, as discussed in the review by Porter and others (2005). The pollution threats include point-sources, such as municipal wastewater (Northern District, Hagatna, Naval Station Guam, and Agat-Santa Rita Waster Water Treatment Plants), cooling water (Tanguisson Steam and Cabras Power Plants), and numerous storm water, ballast water, and tank bottom draw outfalls; nonpoint sources include septic systems, urban runoff, illegal dumping, and groundwater discharges. Poor land-use practices include development without the use of runoff management measures, increased areal extent of impervious surfaces and decreased extent of vegetative barriers, and recreational off-road vehicle use. Furthermore, feral ungulates and illegal wildfires remove protective vegetative cover and generally result in increased soil erosion. While anthropogenic point-sources have been reduced in many areas due to better management practices, nonpoint sources have either stayed constant or increased. Between 1975 and 1999, it is estimated that Guam lost more than a quarter of its tree cover, and more than 750 wildfires each year have resulted in a greater proportion of badlands and other erosion-prone land surfaces with high erosion rates (Forestry and Soil Resources Division, 1999). Approximately 1.8 square kilometers (km2) of Asan Bay, west-central Guam, lies within the National Park Service's (NPS) War-in-the-Pacific National Historical Park's (WAPA) Asan Unit; the bay is the sink for material coming out of the Asan watershed. Anthropogenic modifications of the watersheds adjacent to Asan Bay, which include intentionally-set wildfires, construction, and agriculture (Minton, 2005), are believed to have increased over the past 25

Open-File Report↗

USGS2002

Evaluation of airborne thermal-infrared image data for monitoring aquatic habitats and cultural resources within the Grand Canyon

This study examined thermal-infrared (TIR) image data acquired using the airborne Advanced Thematic Mapper (ATM) sensor in the afternoon of July 25th, 2000 over a portion of the Colorado River corridor to determine the capability of these 100-cm resolution data to address some biologic and cultural resource requirements for GCMRC. The requirements investigated included the mapping of warm backwaters that may serve as fish habitats and the detection (and monitoring) of archaeological structures and natural springs that occur on land. This report reviews the procedure for calibration of the airborne TIR data to obtain surface water temperatures and shows the results for various river reaches within the acquired river corridor. With respect to mapping warm backwater areas, our results show that TIR data need to be acquired with a gain setting that optimizes the range of temperatures found within the water to increase sensitivity of the resulting data to a level of 0.1 °C and to reduce scan-line noise. Data acquired within a two-hour window around maximum solar heating (1:30 PM) is recommended to provide maximum solar heating of the water and to minimize cooling effects of late-afternoon shadows. Ground-truth data within the temperature range of the warm backwaters are necessary for calibration of the TIR data. The ground-truth data need to be collected with good locational accuracy. The derived water-temperature data provide the capability for rapid, wide-area mapping of warm-water fish habitats using a threshold temperature for such habitats. The collected daytime TIR data were ineffective in mapping (detecting) both archaeological structures and natural springs (seeps). The inability of the daytime TIR data to detect archaeological structures is attributed to the low thermal sensitivity (0.3 °C) of the collected data. The detection of subtle thermal differences between geologic materials requires sensitivities of at least 0.1 °C, which can be obtained by most TIR sensors using an appropriate gain setting. Simultaneous data collection for both land and water purposes can be achieved using sensors that collect TIR data in two separate channels, each channel using a gain setting most appropriate for land or water. The detection of archaeological structures and natural water seeps would also be improved by collection of data after sunset, which would require a separate data acquisition from that providing surface water temperature data and therefore additional cost. At this point, the cost for acquiring TIR data is quite high ($620/river-km) compared to the potential benefits of the data, unless reflected-wavelength data are also collected that can satisfy other GCMRC protocol requirements (such as mapping riparian vegetation). This is especially true if multiple data acquisitions are required during the year for temporal analyses of backwater areas. The cost for these data cannot be totally mitigated by its ability to partly replace the need for ground surveys of backwaters because calibration of the TIR data will require some ground-truth data from warm backwater areas (in addition to low-temperature main-stem data). However, the airborne data can provide a product that cannot be approached by ground surveys, that being an instantaneous (2 hour) map of surface water temperature over a 160-km stretch of the Grand Canyon.

Arizona↗