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USGS2026

Environmental tradeoffs of urban stream restoration in Fairfax County, Virginia

Regulatory mandates to improve water quality and stream health have driven substantial investment in stream restoration. Most projects aim to improve channel-floodplain connectivity, reduce sediment erosion, and enhance habitat for aquatic organisms, yet few include adequate pre- and post-restoration monitoring to assess outcomes. Since 2007, Fairfax County, Virginia, and the U.S. Geological Survey have partnered to monitor and evaluate water-quality conditions in Flatlick Branch. In 2018, a 1.72-km reach of stream above the monitoring station was restored using a Natural Channel Design approach. This study applied the Stream Functions Pyramid (SFP) framework to evaluate restoration tradeoffs. Post-restoration, watershed hydrology remained largely unchanged, but channel modifications increased flow capacity, reduced velocity, and further disconnected the channel from the floodplain. Nutrient and sediment reductions exceeded expected amounts, but the removal of over 20 % of riparian tree canopy increased physicochemical variability and the frequency and magnitude of water temperature heatwaves. Post-restoration, state standards for low dissolved oxygen and elevated pH were exceeded 2.5 and 7.5 times more often, respectively. Gross primary production and ecosystem respiration increased and organic matter sources supporting metabolism shifted from allochthonous to autochthonous. Trends in several benthic macroinvertebrate metrics, which were improving prior to construction, have since plateaued or declined, and the fish assemblage shifted from a native minnow dominated community to non-native, warmwater tolerant taxa. This study highlights the need for comprehensive assessments of stream restoration and benefits of using the SFP to understand the consequences and possible tradeoffs of different ecosystem management decisions.

Virginia↗

USGS2020

Cytology reveals diverse cell morphotypes and cellin-cell interactions in normal collector sea urchins Tripneustes gratilla

Echinoderms such as sea urchins are important in marine ecosystems, particularly as grazers, and unhealthy sea urchins can have important ecological implications. For instance, unexplained mortalities of Diadema antillarum in the Caribbean were followed by algal overgrowth and subsequent collapse of coral reef ecosystems. Unfortunately, few tools exist to evaluate echinoderm health, making management of mortalities or other health issues problematic. Hematology is often used to assess health in many animal groups, including invertebrates, but is seldom applied to echinoderms. We used a standard gravitometric technique to concentrate fixed coelomocytes from the collector sea urchin Tripneustes gratilla onto microscope slides, permitting staining and enumeration. Using Romanowsky stain and electron microscopy to visualize cell details, we found that urchin cells could be partitioned into different morphotypes. Specifically, we enumerated phagocytes, phagocytes with perinuclear cytoplasmic dots, vibratile cells, colorless spherule cells, red spherule cells, and red spherule cells with pink granules. We also saw cell-in-cell interactions characterized by phagocytes apparently phagocytizing mainly the motile cells including red spherule cells, colorless spherule cells, and vibratile cells disproportionate to underlying populations of circulating cells. Cell-in-cell interactions were seen in 71% of sea urchins, but comprised <1% of circulating cells. Finally, about 40% of sea urchins had circulating phagocytes that were apparently phagocytizing spicules. The coelomic fluid collection and slide preparation methods described here are simple, field portable, and might be a useful complementary tool for assessing health of other marine invertebrates, revealing heretofore unknown physiological phenomena in this animal group.

Hawaii↗

USGS2010

Global change and water resources in the next 100 years

We are in the midst of a continental-scale, multi-year experiment in the United States, in which we have not defined our testable hypotheses or set the duration and scope of the experiment, which poses major water-resources challenges for the 21st century. What are we doing? We are expanding population at three times the national growth rate in our most water-scarce region, the southwestern United States, where water stress is already great and modeling predicts decreased streamflow by the middle of this century. We are expanding irrigated agriculture from the west into the east, particularly to the southeastern states, where increased competition for ground and surface water has urban, agricultural, and environmental interests at odds, and increasingly, in court. We are expanding our consumption of pharmaceutical and personal care products to historic high levels and disposing them in surface and groundwater, through sewage treatment plants and individual septic systems. These substances are now detectable at very low concentrations and we have documented significant effects on aquatic species, particularly on fish reproduction function. We don’t yet know what effects on human health may emerge, nor do we know if we need to make large investments in water treatment systems, which were not designed to remove these substances. These are a few examples of our national-scale experiment. In addition to these water resources challenges, over which we have some control, climate change models indicate that precipitation and streamflow patterns will change in coming decades, with western mid-latitude North America generally drier. We have already documented trends in more rain and less snow in western mountains. This has large implications for water supply and storage, and groundwater recharge. We have documented earlier snowmelt peak spring runoff in northeastern and northwestern States, and western montane regions. Peak runoff is now about two weeks earlier than it was in the first half of the 20th century. Decreased summer runoff affects water supply for agriculture, domestic water supply, cooling needs for thermoelectric power generation, and ecosystem needs. In addition to the reduced volume of streamflow during warm summer months, less water results in elevated stream temperature, which also has significant effects on cooling of power generating facilities and on aquatic ecosystem needs. We are now required to include fish and other aquatic species in negotiation over how much water to leave in the river, rather than, as in the past, how much water we could remove from a river. Additionally, we must pay attention to the quality of that water, including its temperature. This is driven in the US by the Endangered Species Act and the Clean Water Act. Furthermore, we must now better understand and manage the whole hydrograph and the influence of hydrologic variability on aquatic ecosystems. Man has trimmed the tails off the probability distribution of flows. We need to understand how to put the tails back on but can’t do that without improved understanding of aquatic ecosystems. Sea level rise presents challenges for fresh water extraction from coastal aquifers as they are compromised by increased saline intrusion. A related problem faces users of ‘run-of-the-river’ water-supply intakes that are threatened by a salt front that migrates further upstream because of higher sea level. We face significant challenges with water infrastructure. The U.S. has among the highest quality drinking water in the world piped to our homes. However, our water and sewage treatment plants and water and sewer pipelines have not had adequate maintenance or investment for decades. The US Environmental Protection Agency estimates that there are up to 3.5M illnesses per year from recreational contact with sewage from sanitary sewage overflows. Infrastructure investment needs have been put at 5 trillion nationally. Global change and water resources c

Conference Paper↗

USGS2014

An ecological response model for the Cache la Poudre River through Fort Collins

The Poudre River Ecological Response Model (ERM) is a collaborative effort initiated by the City of Fort Collins and a team of nine river scientists to provide the City with a tool to improve its understanding of the past, present, and likely future conditions of the Cache la Poudre River ecosystem. The overall ecosystem condition is described through the measurement of key ecological indicators such as shape and character of the stream channel and banks, streamside plant communities and floodplain wetlands, aquatic vegetation and insects, and fishes, both coolwater trout and warmwater native species. The 13- mile-long study area of the Poudre River flows through Fort Collins, Colorado, and is located in an ecological transition zone between the upstream, cold-water, steep-gradient system in the Front Range of the Southern Rocky Mountains and the downstream, warm-water, low-gradient reach in the Colorado high plains. The City wanted to better understand the ecological response of the Poudre River ecosystem to potential changes in stream flow and other physical parameters through the conceptual framework of a multivariable integrated model. This goal was met through the use of a probabilistic model based on Bayesian concepts. This construct allowed the integration of a wide range of data and expert opinion (as informed by local data) to predict potential changes to ecosystem conditions under various flow scenarios. Nine flow scenarios representing past, present, and possible future hydrology were developed as the primary model input. Both reach-scale drivers such as stream channel conditions and pollutant loads, as well as ecological conditions, including species composition, interactions, and habitat requirements influenced model-predicted ecosystem outcomes. Model output consisted of probability distributions for eight ecological indicators collectively representing the physical setting, aquatic life, and riparian habitats of the river ecosystem. We are confident in model predictions related to probable trends, relative magnitude of changes and potential ecosystem responses to changing flow conditions, though data availability and the process of converting diverse data types into a common unit (probabilities) limit precision of individual results. Key findings suggest that: The present ecological function of the Poudre River is altered as a result of more than 150 years of human influences that include highly managed flows, urbanization, gravel mining, channelization and urban and industrial encroachment in the floodplain, underscoring the vulnerable and complex character of the Poudre River; A continuation of today’s flow management will lead to ongoing changes in ecosystem condition, and additional water depletions will compromise ecological conditions; High flows play an essential role in maintaining and improving the aquatic and riparian condition of the river; Adequate flows in base-flow periods are critical to desirable water quality, and thriving fish and insect populations; Improvement of native aquatic life is possible if issues related to channel modifications, siltation, invasive species, and base and high flow conditions are managed properly; The present confined river channel and modified flows has reduced the potential for a keystone and iconic species, plains cottonwood, to be self-sustaining in the study area; The streamside corridor retains the potential to support a functioning riparian forest that provides important ecological services if periodic floodplain inundation occurs. Environmental flows that combine stable and adequate flows in base-flow periods with occasional rejuvenating high flows that meet target levels defined in this study are likely improve all biological indicators across the system. ERM test scenarios that include both stable base flows and rejuvenating high flows indicate that substantial improvements in the river ecosystem can be achieved with improved management of flow volumes similar to those observed in the river during the last half century of intensive water development. These results underscore the possibility of improving the river ecosystem through active management while still maintaining the Poudre’s diverse economic benefits and role as a working river. The ERM was designed to represent the multi-dimensional ecological character of the contemporary urban Poudre River. It provides a scientific foundation that can serve as a decision support tool and foster a more informed community discussion about the future of the river as it provides a better understanding of the likely response of the Poudre River ecosystem to environmental flow management and other stewardship activities. In particular, model results can assist managers in developing specific management actions to achieve desirable goals for key indicators of river health.

Colorado↗

USGS2021

Synthesis of data and studies relating to Delta Smelt biology in the San Francisco Estuary, emphasizing water year 2017

In the San Francisco Estuary (SFE), the effects of freshwater flow on the aquatic ecosystem have been studied extensively over the years and remains a contentious management issue. It is especially contentious with regards to the Delta Smelt (Hypomesus transpacificus), a species endemic to the SFE that has been listed as threatened under the Federal Endangered Species Act and endangered by the State of California. Early studies of Delta Smelt distribution within the SFE suggested that Delta Smelt habitat is determined largely by freshwater flow; however, the exact mechanisms and processes producing such benefits remained unclear. In the summer of 2017, the Flow Alteration Management, Analysis, and Synthesis Team (FLOAT-MAST) was established to analyze, synthesize, and summarize the data collected from the various flow-related monitoring and special studies occurring in 2017(see Table Intro 4). This report will focus on the 2017 summer-fall status of Delta Smelt and its habitat following a record wet year. There has been a long-term decline in the abundance of Delta Smelt associated with a decline in other pelagic fishes. Investigators concluded that the decline has likely been caused by the interactive effects of several causes, including changes in both physical and biotic habitats, many of which are tied to amount and timing of freshwater flow. For this report, we formulated a number of basic predictions about the likely effects of high flows in 2017 on Delta Smelt and their habitat (Table 3). We use a qualitative weight of evidence approach to evaluate whether these predictions were supported by available data. Data sources included a variety of long-term monitoring surveys conducted by Interagency Ecological Program (IEP) agencies, as well as model outputs. Delta Smelt population, health, and life history metrics rarely responded as predicted. Water temperature appears to have a stronger effect on Delta Smelt growth rate and some metrics of life history diversity than outflow or X2 position. Other life history diversity attributes varied but did not appear to be driven by outflow or temperature. Health status was difficult to interpret. Low prevalence of lesions and improved nutritional condition during the drought was contradicted by declining overall population levels. Because of the sparse catches of Delta Smelt in the post-POD years, we consider the data insufficient to reach firm conclusions about the predictions concerning range and distribution of Delta Smelt, especially in the fall. The prediction of high survival was not supported. The 2017 Delta Smelt year class began with poor recruitment in spring of 2017 and below average survival for spring to summer and summer to fall. Thus, low production and low survival led to low abundance of all life stages. During the fall to winter period survival improved, yet the resulting adults were low in number. Foraging success of the fish captured, as measured by stomach fullness, was high for juveniles and adults in 2017 relative to recent years associated with the higher densities of common zooplankton prey that occurred in 2017.

California↗

USGS2023

Ammonia and aquatic ecosystems – A review of global sources, biogeochemical cycling, and effects on fish

The purpose of this review is to better understand the full life cycle and influence of ammonia from an aquatic biology perspective. While ammonia has toxic properties in water and air, it also plays a central role in the biogeochemical nitrogen (N) cycle and regulates mechanisms of normal and abnormal fish physiology. Additionally, as the second most synthesized chemical on Earth, ammonia contributes economic value to many sectors, particularly fertilizers, energy storage, explosives, refrigerants, and plastics. But, with so many uses, industrial N 2 -fixation effectively doubles natural reactive N concentrations in the environment. The consequence is global, with excess fixed nitrogen driving degradation of soils, water, and air; intensifying eutrophication, biodiversity loss, and climate change; and creating health risks for humans, wildlife, and fisheries. Thus, the need for ammonia research in aquatic systems is growing. In response, we prepared this review to better understand the complexities and connectedness of environmental ammonia. Even the term “ammonia” has multiple meanings. So, we have clarified the nomenclature, identified units of measurement, and summarized methods to measure ammonia in water. We then discuss ammonia in the context of the N-cycle, review its role in fish physiology and mechanisms of toxicity, and integrate the effects of human N-fixation, which continuously expands ammonia's sources and uses. Ammonia is being developed as a carbon-free energy carrier with potential to increase reactive nitrogen in the environment. With this in mind, we review the global impacts of excess reactive nitrogen and consider the current monitoring and regulatory frameworks for ammonia. The presented synthesis illustrates the complex and interactive dynamics of ammonia as a plant nutrient, energy molecule, feedstock, waste product, contaminant, N-cycle participant, regulator of animal physiology, toxicant, and agent of environmental change. Few molecules are as influential as ammonia in the management and resilience of Earth's resources.

Science of the Total Environment↗

USGS2020

Relation of fish intersex to contaminants in riverine sport fishes

Endocrine active compounds (EACs) are pollutants that have been recognized as an emerging and widespread threat to aquatic ecosystems globally. Intersex, the presence of female germ cells within a predominantly male gonad, is considered a biomarker of endocrine disruption caused by EACs. We measured a suite of EACs and assessed their associated impacts on fish intersex occurrence and severity in a large, regulated river system in North Carolina and South Carolina, USA. Our specific objective was to determine the relationship of contaminants in water, sediment, and fish tissue with the occurrence and severity of the intersex condition in wild, adult black bass ( Micropterus ), sunfish ( Lepomis ), and catfish (Ictaluridae) species at 11 sites located on the Yadkin-Pee Dee River. Polycyclic aromatic hydrocarbons (PAHs), ethinylestradiol (EE2), and heavy metals were the most prevalent contaminants that exceeded effect levels for the protection of aquatic organisms. Fish intersex condition was most frequently observed and most severe in black basses and was less frequently detected and less severe in sunfishes and catfishes. The occurrence of the intersex condition in fish showed site-related effects, rather than increasing longitudinal trends from upstream to downstream. Mean black bass and catfish tissue contaminant concentrations were higher than that of sunfish, likely because of the latter's lower trophic position in the food web. Principal component analysis identified waterborne PAHs as the most correlated environmental contaminant with intersex occurrence and severity in black bass and sunfish. As indicated by the intersex condition, EACs have adverse but often variable effects on the health of wild sport fishes in this river, likely due to fluctuations in EAC inputs and the dynamic nature of the riverine system. These findings enhance the understanding of the relationship between contaminants and fish health and provide information to guide ecologically comprehensive conservation and management decisions.

North Carolina, South Carolina↗

USGS2022

Potential health effects of contaminant mixtures from point and nonpoint sources on fish and frogs in the New Jersey Pinelands

Aquatic ecosystems convey complex contaminant mixtures from anthropogenic pollution on a global scale. Point (e.g., municipal wastewater) and nonpoint sources (e.g., stormwater runoff) are both drivers of contaminant mixtures in aquatic habitats. The objectives of this study were to identify the contaminant mixtures present in surface waters impacted by both point and nonpoint sources, to determine if aquatic biota (amphibian and fish) health effects (testicular oocytes and parasites) occurred at these sites, and to understand if differences in biological and chemical measures existed between point (on-stream) and nonpoint sources (off-stream). To accomplish this, water chemistry, fishes, and frogs were collected from 21 sites in the New Jersey Pinelands, United States. Off-stream sites consisted of 3 reference and 10 degraded wetlands. On-stream sites consisted of two reference lakes and six degraded steams/lakes (four sites above and two sites below wastewater outfalls). Surface water was collected 4 times at each site and analyzed for 133 organic and inorganic contaminants. One native and five non-native fish species were collected from streams/lakes and native green frogs from wetlands (ponds and stormwater basins). Limited differences in contaminant concentrations were observed in reference and degraded wetlands but for streams/lakes, results indicated that landscape alteration, (upland agricultural and developed land) was the primary driver of contaminant concentrations rather than municipal wastewater. Incidence of estrogenic endocrine disruption (intersex) was species dependent with the highest prevalence observed in largemouth bass and black crappie and the lowest prevalence observed in green frogs and tessellated darters. Parasite prevalence was site and species dependent. Prevalence of eye parasites increased with increasing concentrations of industrial, mycotoxin, and cumulative inorganic contaminants. These findings are critical to support the conservation, protection, and management of a wide range of aquatic species in the Pinelands and elsewhere as habitat loss, alteration, and fragmentation increase with increasing development.

New Jersey↗

USGS2016

Spatial and temporal patterns of mercury concentrations in freshwater fish across the Western United States and Canada

Methylmercury contamination of fish is a global threat to environmental health. Mercury (Hg) monitoring programs are valuable for generating data that can be compiled for spatially broad syntheses to identify emergent ecosystem properties that influence fish Hg bioaccumulation. Fish total Hg (THg) concentrations were evaluated across the Western United States (US) and Canada, a region defined by extreme gradients in habitat structure and water management. A database was compiled with THg concentrations in 96,310 fish that comprised 206 species from 4262 locations, and used to evaluate the spatial distribution of fish THg across the region and effects of species, foraging guilds, habitats, and ecoregions. Areas of elevated THg exposure were identified by developing a relativized estimate of fish mercury concentrations at a watershed scale that accounted for the variability associated with fish species, fish size, and site effects. THg concentrations in fish muscle ranged between 0.001 and 28.4 (μg/g wet weight (ww)) with a geometric mean of 0.17. Overall, 30% of individual fish samples and 17% of means by location exceeded the 0.30 μg/g ww US EPA fish tissue criterion. Fish THg concentrations differed among habitat types, with riverine habitats consistently higher than lacustrine habitats. Importantly, fish THg concentrations were not correlated with sediment THg concentrations at a watershed scale, but were weakly correlated with sediment MeHg concentrations, suggesting that factors influencing MeHg production may be more important than inorganic Hg loading for determining fish MeHg exposure. There was large heterogeneity in fish THg concentrations across the landscape; THg concentrations were generally higher in semi-arid and arid regions such as the Great Basin and Desert Southwest, than in temperate forests. Results suggest that fish mercury exposure is widespread throughout Western US and Canada, and that species, habitat type, and region play an important role in influencing ecological risk of mercury in aquatic ecosystems.

Science of the Total Environment↗

USGS2018

Agriculture — A river runs through it — The connections between agriculture and water quality

Sustaining the quality of the Nation’s water resources and the health of our diverse ecosystems depends on the availability of sound water-resources data and information to develop effective, science-based policies. Effective management of water resources also brings more certainty and efficiency to important economic sectors. Taken together, these actions lead to immediate and longterm economic, social, and environmental benefits that make a difference to the lives of the almost 400 million people projected to live in the United States by 2050. In 1991, Congress established the U.S. Geological Survey National Water-Quality Assessment (NAWQA) to address where, when, why, and how the Nation’s water quality has changed, or is likely to change in the future, in response to human activities and natural factors. Since then, NAWQA has been a leading source of scientific data and knowledge used by national, regional, state, and local agencies to develop science-based policies and management strategies to improve and protect water resources used for drinking water, recreation, irrigation, energy development, and ecosystem needs. Plans for the third decade of NAWQA (2013–23) address priority water-quality issues and science needs identified by NAWQA stakeholders, such as the Advisory Committee on Water Information and the National Research Council, and are designed to meet increasing challenges related to population growth, increasing needs for clean water, and changing land-use and weather patterns. This report is one of a series of publications, The Quality of Our Nation’s Waters , which describes major findings of the NAWQA Project on water-quality issues of regional and national concern and provides science-based information for assessing and managing the quality of our groundwater resources. Other reports in this series focus on occurrence and distribution of nutrients, pesticides, and volatile organic compounds in streams and groundwater, the effects of contaminants and stream-flow alteration on the condition of aquatic communities in streams, and on the quality of groundwater from private domestic and public supply wells. Each reports builds toward a more comprehensive understanding of the quality of regional and national water resources. All NAWQA reports are available online ( https://water.usgs.gov/nawqa/bib/ ). We hope this publication will provide you with insights and information to meet your water-resource needs and will foster increased citizen awareness and involvement in the protection and restoration of our Nation’s waters. The information in this report is intended primarily for those interested or involved in resource management and protection, conservation, regulation, and policymaking at the regional and national levels.

Circular↗

USGS1998

Water quality in the central Columbia Plateau, Washington and Idaho, 1992-95

Water quality in the Central Columbia Plateau of eastern Washington and western Idaho has been adversely affected by agriculture, especially in irrigated areas, according to the results of a five-year investigation by the U. S. Geological Survey (USGS). Some improvements, however, are noticeable, such as less sediment being washed into streams. These improvements may be the result of increased use of best management practices (BMPs) by area farmers. Areas with intensive fertilizer use and irrigation, such as in the Columbia Basin Irrigation Project (CBIP), showed the greatest impacts on ground-water quality. (The CBIP includes parts of Franklin, Grant, and Adams counties in eastern Washington.) <Shallow wells, generally those less than 150 feet deep, are the most susceptible to contamination, the USGS report says. A reassuring aspect of this finding, however, is that many public water supplies draw from wells at greater depths and are less susceptible to contamination from agricultural practices. From the standpoint of human health, we were most concerned about checking for nitrate and pesticides in drinking water,' said Sandy Williamson, USGS hydrologist and chief of the study. 'We found nitrate levels exceeding the maximum contaminant level in about 20 percent of all wells.' (A maximum contaminant level-or MCL-is a drinking water regulatory standard that is set by the U.S. Environmental Protection Agency.) 'The story on pesticides is a mixed bag,' Williamson said. 'We found at least one pesticide in nearly half of the drinking water wells sampled, but pesticide levels were only a very small fraction of their MCLs.' As a cautionary note, however, Williamson said that about half of the pesticides detected in Central Columbia Plateau wells do not have MCLs established. A lack of information makes it difficult to assess the significance of finding pesticides in drinking water. 'As scientists, we don't know enough yet about what happens when these pesticides are combined,' he said. 'In some of the very shallow wells that the USGS installed for monitoring purposes, we found up to seven different pesticides.' Encouraging news is that none of the newer pesticides, which break down more rapidly in the environment, were found at concentrations exceeding MCLs. Compounds that exceed drinking water standards were found in only 1 percent of the wells sampled-and those compounds have not been sold as pesticides since the mid-1980s. However, agricultural impacts on water quality go beyond the concerns for drinking water-the aquatic ecosystem of the plateau also has been significantly affected. 'Very little surface water is used for drinking water in this area, but fish are harmed by decreased stream-water quality,' said Mark Munn, the biologist for the USGS study. 'Pesticides and habitat degradation are the main concerns.' He noted that stream sampling by the USGS showed seven currently used pesticides at concentrations above the limits recommended for protecting aquatic life. Soil erosion, a long-term problem for farmers in the Palouse River Basin, transports some soil to streams, degrading habitat and carrying with it older pesticides and their breakdown products. A breakdown product of the banned insecticide DDT was found in both streambed sediment and bottom fish at concentrations exceeding guidelines for the protection of aquatic life. 'Another problem for fish habitat is excessive plant growth caused by high levels of nutrients in streams,' said Munn, who explained that these nutrients enter streams in runoff from agricultural fields and discharge from urban wastewater treatment plants. Some agricultural practices, such as allowing cattle to graze near streams, are associated with higher rates of erosion. However, increased use of BMPs may improve water quality of the plateau. The USGS study showed that use of sprinkler or drip rather than furrow irrigation has decreased soil erosion in the CBIP area. In the Palouse, erosion

Circular↗

USGS2008

Response of fish populations to natural channel design restoration in streams of the Catskill Mountains, New York

Many streams and rivers throughout North America have been extensively straightened, widened, and hardened since the middle 1800s, but related effects on aquatic ecosystems have seldom been monitored, described, or published. Beginning in the early 1990s, reach-level restoration efforts began to base projects on natural channel design (NCD) techniques and Rosgen's (1994b, 1996) river classification system in an effort to duplicate or mimic stable reference reach geomorphology. Four reaches in three streams of the Catskill Mountains, New York, were restored from 2000 to 2002 using NCD techniques to decrease bed and bank erosion rates, decrease sediment loads, and improve water quality. The effects of restoration on the health of fish assemblages were assessed through a before-after, control-impact (BACI) study design to quantify the net changes in population and community indices at treatment reaches relative to index changes at unaltered reference reaches from 1999 to 2004. After restoration, community richness and biomass at treatment reaches increased by more than one-third. Changes in fish communities were caused mainly by shifts in dominant species populations; fish community biomass and total fish abundance were generally dominated by daces or daces and sculpins before restoration and by one or more salmonid species after restoration. Density and biomass of eastern blacknose dace Rhinichthys atratulus, longnose dace R. cataractae, and slimy sculpin Cottus cognatus did not change appreciably, whereas net salmonid density and biomass increased substantially after restoration. These changes were driven primarily by large increases in populations of brown trout Salmo trutta. The findings demonstrate that the structure, function, and ultimately the health of resident fish populations and communities can be improved, at least over the short term, through NCD restoration in perturbed streams of the Catskill Mountains. ?? Copyright by the American Fisheries Society 2008.

North American Journal of Fisheries Management↗

USGS2022

Framework for the development of the Columbia River mainstem fish tissue and water quality monitoring program - Bonneville Dam to Canadian border

The Columbia River provides important cultural, economic, and ecological services to a significant portion of the United States. Anadromous and resident fish species and other wildlife are integrated into the cultural traditions of all Tribes in the Columbia River Basin. Salmon, lamprey, sturgeon, and resident fish are an integral part of Tribal religion, culture, and physical sustenance. Despite concerns about the effect of contaminants on the aquatic ecosystem, the disproportionate effects of contaminants on members of Tribal sovereignties, and the known effects of contaminants on species protected under the Endangered Species Act, efforts to address toxic chemical pollution in the Columbia River have been limited. The lack of a dedicated contaminant monitoring program impedes evaluation and decision making regarding the health of the Columbia River ecosystem, as well as human health for Tribal members and others that consume fish and other biota from the Columbia River. The purpose of this framework is to provide guidance for the development of a long-term program (Program) that provides the basis for assessing the status and trends of contaminants in fish, sediment, water, and invertebrates along the 962-kilometer length of the Columbia River from the Bonneville Dam upriver to the Canadian Border (Figure ES1). This framework will focus on four persistent and bioaccumulative classes of toxic contaminants: • Mercury • Polychlorinated biphenyls (PCBs) • Dichlorodiphenyltrichloroethane (DDT) • Polybrominated diphenyl ethers (PBDEs) Media of interest in this framework include anadromous and resident fish, sediment, invertebrates, biofilm, and surface water. Future consideration of additional contaminants could include pesticides, per or poly-fluoroalkyl substances, 6PPD-quinone, and contaminants of emerging concern (CECs), which comprises a diverse group of anthropogenic chemicals that include thousands of pharmaceuticals, hormones, illicit drugs, new pesticides, personal care products, flame retardants, artificial sweeteners, perfluorinated compounds, disinfection byproducts, ultraviolet filters, and other industrial chemicals. This framework includes the vision, goals, and objectives for the Program. The vision for the Program is that it will provide the basis for assessing the status and trends of contaminants in the Columbia River to guide ecosystem recovery resulting in clean, healthy fish for current and future generations . The goals of the Program are to 1) conduct long-term monitoring to assess the spatial and temporal status and trends of toxics in fish, water, sediment, and other potential media in the Columbia River mainstem, from Bonneville Dam to the Canadian Border in perpetuity, 2) stimulate conversion of science into action by providing information to facilitate future decision making that improves ecosystem function and reduces contaminants in all levels of the food chain, and 3) adaptively manage the Program to address new key questions, incorporate new and emerging science advancements, and respond to community information needs. To facilitate achieving these goals, this framework provides details on technical planning; community outreach and engagement; and adaptive management to promote understanding and improve future decision making over the long-term, including updating the Program with new and emerging science and community needs. Additionally, data associated with the Program will be made available to the public through the EPA Water Quality Exchange (https://www.epa.gov/waterdata/water-quality-data). Documents and other materials associated with the Program can be accessed via a website hosted by Yakama Nation Fisheries (https://yakamafish-nsn.gov/restore/projects/columbia-river-mainstem- water-quality-monitoring-program). Although the Program is limited to the Columbia River upstream of the Bonneville Dam, collaboration with other entities that monitor contaminants in the Columbia River Basin, including the Columbia River estuary below Bonneville Dam, are also an important component of outreach. Our goal is to encourage efforts to ensure data comparability across programs and recognize that the growth and adaptive management of the Program considers basin-wide monitoring developments.

Oregon, Washington↗

USGS2011

Setting limits: Using air pollution thresholds to protect and restore U.S. ecosystems

More than four decades of research provide unequivocal evidence that sulfur, nitrogen, and mercury pollution have altered, and will continue to alter, our nation's lands and waters. The emission and deposition of air pollutants harm native plants and animals, degrade water quality, affect forest productivity, and are damaging to human health. Many air quality policies limit emissions at the source but these control measures do not always consider ecosystem impacts. Air pollution thresholds at which ecological effects are observed, such as critical loads, are effective tools for assessing the impacts of air pollution on essential ecosystem services and for informing public policy. U.S. ecosystems can be more effectively protected and restored by using a combination of emissions-based approaches and science-based thresholds of ecosystem damage. Based on the results of a comprehensive review of air pollution thresholds, we conclude: ??? Ecosystem services such as air and water purification, decomposition and detoxification of waste materials, climate regulation, regeneration of soil fertility, production and biodiversity maintenance, as well as crop, timber and fish supplies are impacted by deposition of nitrogen, sulfur, mercury and other pollutants. The consequences of these changes may be difficult or impossible to reverse as impacts cascade throughout affected ecosystems. ??? The effects of too much nitrogen are common across the U.S. and include altered plant and lichen communities, enhanced growth of invasive species, eutrophication and acidification of lands and waters, and habitat deterioration for native species, including endangered species. ??? Lake, stream and soil acidification is widespread across the eastern United States. Up to 65% of lakes within sensitive areas receive acid deposition that exceeds critical loads. ??? Mercury contamination adversely affects fish in many inland and coastal waters. Fish consumption advisories for mercury exist in all 50 states and on many tribal lands. High concentrations of mercury in wildlife are also widespread and have multiple adverse effects. ??? Air quality programs, such as those stemming from the 1990 Clean Air Act Amendments, have helped decrease air pollution even as population and energy demand have increased. Yet, they do not adequately protect ecosystems from long-term damage. Moreover they do not address ammonia emissions. ??? A stronger ecosystem basis for air pollutant policies could be established through adoption of science-based thresholds. Existing monitoring programs track vital information needed to measure the response to policies, and could be expanded to include appropriate chemical and biological indicators for terrestrial and aquatic ecosystems and establishment of a national ecosystem monitoring network for mercury. The development and use of air pollution thresholds for ecosystem protection and management is increasing in the United States, yet threshold approaches remain underutilized. Ecological thresholds for air pollution, such as critical loads for nitrogen and sulfur deposition, are not currently included in the formal regulatory process for emissions controls in the United States, although they are now considered in local management decisions by the National Park Service and U.S. Forest Service. Ecological thresholds offer a scientifically sound approach to protecting and restoring U.S. ecosystems and an important tool for natural resource management and policy. ?? The Ecological Society of America.

Issues in Ecology↗

USGS2001

Macroinvertebrate instream flow studies after 20 years: A role in stream management and restoration

Over the past two decades of refinement and application of instream flow evaluations, we have examined the hydraulic habitat of aquatic macroinvertebrates in a variety of conditions, along with the role of these macroinvertebrates in sustaining ecosystem integrity. Instream flow analyses assume that predictable changes in channel flow characteristics can, in turn, be used to predict the change in the density or distribution of lotic species or, more appropriately, the availability of useable habitat for those species. Five major hydraulic conditions most affect the distribution and ecological success of lotic biota: suspended load, bedload movement, and water column effects, such as turbulence, velocity profile, and substratum interactions (near-bed hydraulics). The interactions of these hydraulic conditions upon the morphology and behavior of the individual organisms govern the distribution of aquatic biota. Historically, management decisions employing the Physical Habitat Simulation (PHABSIM) have focused upon prediction of available habitat for life stages of target fish species. Regulatory agencies have rarely included evaluation of benthos for flow reservations. Although ‘taxonomic discomfort’ may be cited for the reluctant use or creation of benthic criteria, we suggest that a basic misunderstanding of the links between benthic macroinvertebrate and the fish communities is still a problem. This is derived from the lack of a perceived ‘value’ that can be assigned to macroinvertebrate species. With the exception of endangered mussel species (for which PHABSIM analysis is probably inappropriate), this is understandable. However, it appears that there is a greater ability to predict macroinvertebrate distribution (that is, a response to the change in habitat quality or location) and diversity without complex population models. Also, habitat suitability criteria for water quality indicator taxa (Ephemeroptera, Plecoptera, and Trichoptera; the so-called ‘EPTs’) may also provide additional management options to stream regulators. The greatest application for macroinvertebrate criteria will be in low-order streams where a more immediate link to fish communities can be established. We present an example from Queens Creek, in North Carolina, USA, in which monthly allocations required to preserve the integrity of the benthic macroinvertebrate community were significantly higher than for the target benthic fish species, Cottus bairdi . In the months when both Cottus and community diversity of macroinvertebrates were the ‘bottleneck’ life stages, preservation of only fish species could result in an additional 5–25% loss in macroinvertebrate habitat. We suggest that, as there becomes an increased emphasis on maintaining macroinvertebrates as monitors of stream health, there will be a concurrent emphasis on incorporating hydraulic habitat conditions as a part of bioassessment.

Regulated Rivers: Research & Management↗

USGS2010

Investigation of submarine groundwater discharge along the tidal reach of the Caloosahatchee River, southwest Florida

The tidal reach of the Caloosahatchee River is an estuarine habitat that supports a diverse assemblage of biota including aquatic vegetation, shellfish, and finfish. The system has been highly modified by anthropogenic activity over the last 150 years (South Florida Water Management District (SFWMD), 2009). For example, the river was channelized and connected to Lake Okeechobee in 1881 (via canal C-43). Subsequently, three control structures (spillway and locks) were installed for flood protection (S-77 and S-78 in the 1930s) and for saltwater-intrusion prevention (S-79, W.P. Franklin Lock and Dam in 1966). The emplacement of these structures and their impact to natural water flow have been blamed for water-quality problems downstream within the estuary (Flaig and Capece, 1998; SFWMD, 2009). Doering and Chamberlain (1999) found that the operation of these control structures caused large and often rapid variations in salinity during various times of the year. Variable salinities could have deleterious impacts on the health of organisms in the Caloosahatchee River estuary. Flow restriction along the Caloosahatchee has also been linked to surface-water eutrophication problems (Doering and Chamberlain, 1999; SFWMD, 2009) and bottom-sediment contamination (Fernandez and others, 1999). Sources of nutrients (nitrogen and phosphorous) that cause eutrophication are primarily from residential sources and agriculture, though wastewater-treatment-plant discharges can also play a major role (SFWMD, 2009). The pathway for many of these nutrients is by land runoff and direct discharge from stormwater drains. An often overlooked source of nutrients and other chemical constituents is from submarine groundwater discharge (SGD). SGD can be either a diffuse or point source (for example, submarine springs) of nutrients and other chemical constituents to coastal waters (Valiela and others, 1990; Swarzenski and others, 2001; 2006; 2007; 2008). SGD can be composed of either fresh or marine water or various mixed ratios of fresh and marine water (Martin and others, 2007). In coastal areas where water-table elevations (hydraulic gradients) are steep, such as in Hood Canal, Washington (Swarzenski and others, 2007; Simonds and others, 2008), groundwater entering the coastal marine waters can be fresh (~1-4 parts per thousand, ppt). SGD in coastal locations that have low relief (low hydraulic gradients) such as the study area or other locations in Florida are typically driven by tidal pumping (Reich and others, 2002; 2008; Swarzenski and others, 2008), and water advecting into surface water is composed of recirculated marine water mixed with either fresh or brackish groundwaters. The importance of SGD in the delivery of nutrients and trace elements to coastal environments has been shown to be both beneficial and deleterious to ecosystem health (Valiela and others, 1990). The logical step in studying SGD is to map areas where SGD occurs. Methods such as continuous surface-water radon-222 ( 222 Rn) mapping and electrical resistivity (continuous resistivity profiles, CRP) have been developed and used to identify potential SGD sites (Dulaiova and others, 2005; Swarzenski and others 2004; 2006; 2007; 2008; Reich and others, 2008). CRP data record subsurface, bulk-resistivity measurements to depths up to 25 meters (m). The bulk resistivity can be representative of changes in porewater salinity or in lithology (Reich and others, 2008; Swarzenski and others, 2008). Radon-222 (half-life = 3.28 days) is a natural tracer of groundwater, because sediments and rocks, containing uranium-bearing materials such as limestone and phosphatic material, continually produce 222 Rn. Rn-222 (also referred to simply as radon) is an ideal tracer, because there is a constant source. Since radon is a gas, 222 Rn does not build up in the surface water but rather evades directly to the atmosphere (Burnett and Dulaiova, 2003; Burnett and others, 2003; Dulaiova and Burnett, 2006).

Florida↗

USGS2019

Using the precipitation-runoff modeling system to predict seasonal water availability in the upper Klamath River basin, Oregon and California

Accurate forecasts of the streamflow expected during late spring and summer in the Upper Klamath River Basin in southern-central Oregon and northern California are used by water management agencies to balance water allocations for agriculture, aquatic habitat, and hydropower-production needs. Streamflow forecasts are also used by irrigation farmers for planning. The forecasts are typically made twice a month starting as early in the water year as December. Multiple regression equations relating real-time snowpack and precipitation conditions to seasonal streamflow volumes have been used for many years in forecasting. However, with warming temperature trends and lower snowpack, such forecasts based on historical data could become less reliable in the future. If the timing and relation of snowpack and precipitation are outside of the range of the historical data used to create the equations, the forecasts become extrapolations. Statistical forecast equations are also limited in their ability to forecast streamflow in groundwater-dominated basins having inter-annual lag. As an additional method for seasonal streamflow forecasting, a physical-process-based hydrologic model employing the Precipitation-Runoff Modeling System (PRMS) was developed in cooperation with the U.S. Bureau of Reclamation for the Upper Klamath Basin in this study. The model was calibrated for the portion of the basin draining into Upper Klamath Lake. PRMS is a deterministic, distributed-parameter, physical-process-based modeling system developed by the U.S. Geological Survey. It simulates daily streamflow, snow, solar radiation, evapotranspiration, surface-water, and groundwater processes within the basin. A model calibration and validation period for water years 2000–15 and water years 1984–99, respectively, was used. The model was calibrated and validated using measured streamflow, snowpack, evapotranspiration, and solar radiation data sets. Interpolated daily precipitation and air temperature data from 32 meteorological stations within and surrounding the Upper Klamath Basin were used as model input. Performance statistics, used to evaluate how well simulated daily streamflow matched with measured streamflow included percent bias, percent relative error, and root-mean-square error. The statistics were computed annually, monthly, for October–March, and for April–September. With the exception of the October–March period, percent bias statistics were all within plus or minus 5-percent for both the calibration and validation periods. Limitations to using the model are error in the precipitation and air temperature input time series data, which include measurement error and error in the spatial interpolation method. Other errors include measured daily streamflow data, which were adjusted for consumptive use losses to make them more closely resemble natural streamflow for calibration. The model developed for the Upper Klamath Basin can be used to forecast streamflow from the Sprague and Williamson River Basins and inflow to Upper Klamath Lake. Reliable forecasts at these locations are needed for managing water for irrigation, ecosystem health, and power production. Using the models in a forecast application requires assembling model input data sets of anticipated daily precipitation and minimum and maximum air temperature for the period after the date the forecast is made and the end of the forecasted period. These climate data sets can be based on historical or synthetic records, at the discretion of the forecaster. With the Ensemble Streamflow Prediction method, a suite of streamflow scenarios is simulated using multiple years of climate data as model input. The forecasted streamflow is determined from knowing the exceedance probabilities of the simulated streamflows. In this study, the model and the Ensemble Streamflow Prediction method were used to forecast the volume of inflow to Upper Klamath Lake for a 6-month period from April 1, 2015, to September 30, 2015, using a range of climate data sets based on El Niño Southern Oscillation (ENSO) criteria. Because 2015 was a warm phase ENSO period, climate data for 10 warm phase ENSO years from 1980 to 2010 were used as input to the model. The simulated April–September 2015 UKL inflow volume based on measured 2015 climate data was 482,000 acre-feet, which was very close to the 50th percent exceedance probability computed from 10 simulated scenarios that used warm phase ENSO climate input data from 1980–2010.

California, Oregon↗

USGS2026

Investigation of drivers and sources of potential harmful algal blooms in Lake Anna, Virginia, 2023-24

Algal blooms in freshwater reservoirs are an increasing concern because of the risk to aquatic ecosystem health, recreational use, and water quality. Among the taxa that comprise an algal bloom, cyanobacteria are of particular concern due to the potential to produce toxic compounds which can cause acute and chronic illness in humans if ingested through contaminated water or shellfish. When toxins are above a toxin-specific threshold in the water column, the Commonwealth of Virginia categorizes the bloom as a harmful algal bloom (HAB), distinguishing it from an algal bloom without toxins present. Toxins are of particular concern in bodies of water which serve as major recreational areas, such as Lake Anna in central Virginia. Lake Anna is a 27 km-long and 47 km2 reservoir in central Virginia. Since the Commonwealth of Virginia revised the HAB monitoring framework in 2018, algal bloom advisories for potentially toxigenic blooms have been issued in the western, riverine zone of the reservoir. There were detections of microcystin and anatoxin production but no detections of cylindrospermopsin and saxitoxin production in Lake Anna; however, toxin concentrations were low, at values less than 0.65 µg/L. In 2023, the U.S. Geological Survey, in cooperation with Virginia Department of Environmental Quality, initiated a 19-month intensive and extensive study of western Lake Anna and its tributaries (North Anna River and Pamunkey Creek) to (1) characterize the algal community, biomass, and toxin production; (2) identify potential drivers leading to algal bloom initiation, persistence, and decline; and (3) assess the primary sources of the drivers contributing to algal blooms. Continuous and discrete monitoring of water quality within the lake, watershed inputs, meteorological conditions, and algal communities were monitored. Multiple modeling scenarios identified that the formation and persistence of algal blooms in Lake Anna are driven by interactions among chemical, macro- and micronutrient, and physical factors. Key drivers include total nitrogen, total phosphorus, water temperature, suspended sediment concentration, wind speed, copper, iron, molybdenum, nickel, sodium, and alkalinity. During this study, winter stormflow events delivered the highest loading of macro- and micronutrients from the tributaries to the lake. The lake is a sink for these nutrients in the water column or in the lake-bed sediments. During high-occupancy and recreation periods on the lake in the summer months, boating activity can promote internal loading by the resuspension of the lake-bed sediments, thereby increasing the nutrient availability for algal uptake. Thermal stratification and hypoxic conditions were observed, which can contribute to the passive release of nutrients into the water column, further facilitating algal bloom proliferation. These processes may create a positive feedback loop that supports the formation, persistence, and annual recurrence of algal blooms in the western region of Lake Anna. Continued water-quality monitoring of early warning indicators may improve the detection and forecasting of algal growth in the lake and help managers proactively manage water quality and algal growth.

EarthArXiv↗