Ecosystem variability along the estuarine salinity gradient: Examples from long-term study of San Francisco Bay

Limnology and Oceanography (Wiley) | March 25th, 2017

The salinity gradient of estuaries plays a unique and fundamental role in structuring spatial patterns of physical properties, biota, and biogeochemical processes. We use

The salinity gradient of estuaries plays a unique and fundamental role in structuring spatial patterns of physical properties, biota, and biogeochemical processes. We use variability along the salinity gradient of San Francisco Bay to illustrate some lessons about the diversity of spatial structures in estuaries and their variability over time. Spatial patterns of dissolved constituents (e.g., silicate) can be linear or nonlinear, depending on the relative importance of river-ocean mixing and internal sinks (diatom uptake). Particles have different spatial patterns because they accumulate in estuarine turbidity maxima formed by the combination of sinking and estuarine circulation. Some constituents have weak or no mean spatial structure along the salinity gradient, reflecting spatially distributed sources along the estuary (nitrate) or atmospheric exchanges that buffer spatial variability of ecosystem metabolism (dissolved oxygen). The density difference between freshwater and seawater establishes stratification in estuaries stronger than the thermal stratification of lakes and oceans. Stratification is strongest around the center of the salinity gradient and when river discharge is high. Spatial distributions of motile organisms are shaped by species-specific adaptations to different salinity ranges (shrimp) and by behavioral responses to environmental variability (northern anchovy). Estuarine spatial patterns change over time scales of events (intrusions of upwelled ocean water), seasons (river inflow), years (annual weather anomalies), and between eras separated by ecosystem disturbances (a species introduction). Each of these lessons is a piece in the puzzle of how estuarine ecosystems are structured and how they differ from the river and ocean ecosystems they bridge.

Effect of the South Delta Agricultural Barriers on Emigrating Juvenile Salmonids

California Department of Water Resources (DWR) | November 15th, 2018

The California Department of Water Resources’ (DWR) Temporary Barriers Project (TBP) is an ongoing project that installs, operates, and monitors up to four temporary ro

The California Department of Water Resources’ (DWR) Temporary Barriers Project (TBP) is an ongoing project that installs, operates, and monitors up to four temporary rock-fill barriers constructed in waterways located in the southern portion of the Sacramento-San Joaquin Delta (Delta) near the cities of Tracy and Lathrop in San Joaquin County, California (Figure 1-1). Three of the temporary barriers—Old River at Tracy (ORTB), Middle River (MRB), and Grant Line Canal (GLCB), collectively, the south Delta agricultural barriers (SDABs)—are constructed and operated during the agricultural irrigation season, usually April through November. The SDABs are designed to act as flow control structures, retaining tidal fresh water behind each barrier following a flood tide. The fourth barrier, Head of Old River Barrier (HORB), is installed during the spring and fall as a fish guidance barrier. The HORB is normally installed in the spring to prevent juvenile fall-run San Joaquin River Chinook Salmon (Oncorhynchus tshawytscha) and juvenile Central Valley steelhead (Oncorhynchus mykiss) 2 from emigrating through Old River toward the south Delta water export facilities at the intakes of the State Water Project (SWP) and federal Central Valley Project (CVP). In the fall, the HORB helps to guide adult San Joaquin River Chinook Salmon to spawning locations in the upper watershed. Installation, operation, and removal of the SDABs has the potential to harm, harass, or cause mortality to fish species of management concern to the National Marine Fisheries Service (NMFS), specifically, juvenile fall-run Chinook Salmon which are NMFS Species of Concern (NMFS 2010), juvenile Central Valley steelhead which is a threatened species, an Endangered Species Act (ESA) Section 10j experimental population (63 Federal Register [FR] 13347), and juvenile Green Sturgeon (Acipenser medirostris), also a federally listed threatened species (71 FR 17757). The TBP is implemented in compliance with the terms and conditions of two NMFS Biological Opinions (BiOp) (NMFS 2008, 2009).

Effects Analysis for the Delta Smelt Fall Habitat Action in 2019

U.S. Bureau of Reclamation (USBR) | August 1st, 2019

Effects of ferric sulfate and polyaluminum chloride coagulation enhanced treatment wetlands on Typha growth, soil and water chemistry

Science of the Total Environment (Elsevier) | January 15th, 2019

Land surface subsidence is a concern in many deltas worldwide as it contributes to water quality degradation, loss of fertile land and increased potential for levee f

Land surface subsidence is a concern in many deltas worldwide as it contributes to water quality degradation, loss of fertile land and increased potential for levee failure. As a possible solution to these concerns, on-site coagulation enhanced treatment wetlands (CETWs), coagulation water treatment followed by wetland passage serving as a settling basin, were implemented in a field-scale study located on a subsided island of the Sacramento-San Joaquin Delta in northern California under three treatments; coagulation with polyaluminum chloride (PAC), coagulation with ferric sulfate and an untreated control. Because CETWs offer a relatively novel solution for water quality improvement and subsidence reversal due to its low-infrastructure requirements and in-situ nature, effects from these systems remain uncharted and they may have adverse effects on plant biomass production that also contribute to sediment accretion. This study focuses on the effect CETWs had on the growth of Typha spp.; the dominant vegetation in the wetlands. Plant growth parameters and nutrient content were measured in conjunction with soil, pore water and surface water chemistry. Soil analysis indicated there was no intermixing of newly formed flocs and original soil material. Where there was significant deposition of floc, PAC treatment reduced phosphateconcentrations and ferric sulfate treatment increased total Fe concentrations in surrounding water compared to the control. Results indicated coagulation treatments had no negative effects on Typha leaf nutrient content, Typha growth or allometric parameters. Additionally, no signs of plant toxicity such as necrosis, wilting or chlorosis were observed in any of the treatments. Overall, this study suggests that CETWs are viable treatment option for water quality improvement and sediment accretion while having no negative impact on the growth of Typha plants.

Effects of flow on pesticides in water and zooplankton in the northern Sacramento-San Joaquin Delta

University of California, Davis (UC Davis) | November 1st, 2025

Zooplankton are a key food source for juvenile fishes in estuaries worldwide, including California’s Sacramento–San Joaquin Delta (hereafter Delta); both zooplankton

Zooplankton are a key food source for juvenile fishes in estuaries worldwide, including California’s Sacramento–San Joaquin Delta (hereafter Delta); both zooplankton quality and quantity are critical to ecosystem health. Zooplankton may be affected by pesticides in water and the food web, and the Delta is known to contain complex pesticide mixtures. In this study, we evaluated pesticide concentrations in water and zooplankton in the northern Delta during (1) the summer–fall of 2017, 2018, and 2019, which included periods of augmented pulse flows from agriculture tailwater, and (2) across a full seasonal cycle from May 2019 to March 2020. We quantified changes in pesticide concentration in response to environmental factors. We found that zooplankton showed more frequent detections of hydrophobic pesticides compared to more frequent detections of hydrophilic compounds in water. Pesticide concentrations were influenced by flow, pesticide application, and season, but the effects of these environmental factors differed by habitat (Sacramento River or Yolo Bypass Toe Drain). Pesticides in water responded similarly to environmental factors in the Sacramento River and Yolo Bypass, whereas pesticides in zooplankton responded differently. In water, we found more detections and higher concentrations at higher flows in the Yolo Bypass and Sacramento River, but responses to pesticide application varied by habitat. Alternatively, pesticide concentrations in zooplankton increased in the Yolo Bypass with increasing flow (correlated with flow pulses) and changed seasonally; whereas, pesticide concentrations in zooplankton in the Sacramento River decreased at higher flows, and decreased with or did not respond to higher pesticide application in the watershed. Our study suggests that augmented flows—particularly those using agricultural tailwater—may have unintended negative ecological effects that could partially offset benefits to the food web and fishes in the northern Delta, underscoring the complex interplay among factors that drive increased pesticide exposure.

Effects of Flow on Pesticides in Water and Zooplankton in the Northern Sacramento–San Joaquin Delta

University of California, Davis (UC Davis) | December 19th, 2025

Zooplankton are a key food source for juvenile fishes in estuaries worldwide, including California’s Sacramento–San Joaquin Delta (hereafter Delta); both zooplankton

Zooplankton are a key food source for juvenile fishes in estuaries worldwide, including California’s Sacramento–San Joaquin Delta (hereafter Delta); both zooplankton quality and quantity are critical to ecosystem health. Zooplankton may be affected by pesticides in water and the food web, and the Delta is known to contain complex pesticide mixtures. In this study, we evaluated pesticide concentrations in water and zooplankton in the northern Delta during (1) the summer–fall of 2017, 2018, and 2019, which included periods of augmented pulse flows from agriculture tailwater, and (2) across a full seasonal cycle from May 2019 to March 2020. We quantified changes in pesticide concentration in response to environmental factors. We found that zooplankton showed more frequent detections of hydrophobic pesticides compared to more frequent detections of hydrophilic compounds in water. Pesticide concentrations were influenced by flow, pesticide application, and season, but the effects of these environmental factors differed by habitat (Sacramento River or Yolo Bypass Toe Drain). Pesticides in water responded similarly to environmental factors in the Sacramento River and Yolo Bypass, whereas pesticides in zooplankton responded differently. In water, we found more detections and higher concentrations at higher flows in the Yolo Bypass and Sacramento River, but responses to pesticide application varied by habitat. Alternatively, pesticide concentrations in zooplankton increased in the Yolo Bypass with increasing flow (correlated with flow pulses) and changed seasonally; whereas, pesticide concentrations in zooplankton in the Sacramento River decreased at higher flows, and decreased with or did not respond to higher pesticide application in the watershed. Our study suggests that augmented flows—particularly those using agricultural tailwater—may have unintended negative ecological effects that could partially offset benefits to the food web and fishes in the northern Delta, underscoring the complex interplay among factors that drive increased pesticide exposure.

Effects of salinity on olfactory toxicity and behavioral responses of juvenile salmonids from copper

Aquatic Toxicology (Elsevier) | April 4th, 2016

Dissolved copper is one of the more pervasive and toxic constituents of stormwater runoff and is commonly found in stream, estuary, and coastal marine habitats of juvenil

Dissolved copper is one of the more pervasive and toxic constituents of stormwater runoff and is commonly found in stream, estuary, and coastal marine habitats of juvenile salmon. While stormwater runoff does not usually carry copper concentrations high enough to result in acute lethality, they are of concern because sublethal concentrations of copper exposure have been shown to both impair olfactory function and alter behavior in various species in freshwater. To compare these results to other environments that salmon are likely to encounter, experiments were conducted to evaluate the effects of salinity on the impairment of olfactory function and avoidance of copper. Copper concentrations well within the range of those found in urban watersheds, have been shown to diminish or eliminate the olfactory response to the amino acid, l-serine in freshwater using electro-olfactogram (EOG) techniques. The olfactory responses of both freshwater-phase and seawater-phase coho and seawater-phase Chinook salmon, were tested in freshwater or seawater, depending on phase, and freshwater-phase coho at an intermediate salinity of 10‰. Both 10‰ salinity and full strength seawater protected against the effects of 50 μg copper/L. In addition to impairing olfactory response, copper has also been shown to alter salmon behavior by causing an avoidance response. To determine whether copper will cause avoidance behavior at different salinities, experiments were conducted using a multi-chambered experimental tank. The circular tank was divided into six segments by water currents so that copper could be contained within one segment yet fish could move freely between them. The presence of individual fish in each of the segments was counted before and after introduction of dissolved copper (<20 μg/L) to one of the segments in both freshwater and seawater. To address whether use of preferred habitat is altered by the presence of copper, experiments were also conducted with a submerged structural element. The presence of sub-lethal levels of dissolved copper altered the behavior of juvenile Chinook salmon by inducing an avoidance response in both freshwater and seawater. While increased salinity is protective against loss of olfactory function from dissolved copper, avoidance could potentially affect behaviors beneficial to growth, survival and reproductive success.

Effects of Sea‐Level Rise on Ground Water Flow in a Coastal Aquifer System

National Groundwater Association (NGWA) | January 29th, 2007

The effects of sea‐level rise on the depth to the fresh water/salt water interface were simulated by using a density‐dependent, three‐dimensional numerical ground w

The effects of sea‐level rise on the depth to the fresh water/salt water interface were simulated by using a density‐dependent, three‐dimensional numerical ground water flow model for a simplified hypothetical fresh water lens that is similar to shallow, coastal aquifers found along the Atlantic coast of the United States. Simulations of sea‐level rise of 2.65 mm/year from 1929 to 2050 resulted in an increase in water levels relative to a fixed datum, yet a net decrease in water levels relative to the increased sea‐level position. The net decrease in water levels was much greater near a gaining stream than farther from the stream. The difference in the change in water levels is attributed to the dampening effect of the stream on water level changes in response to sea‐level rise. In response to the decreased water level altitudes relative to local sea level, the depth to the fresh water/salt water interface decreased. This reduction in the thickness of the fresh water lens varied throughout the aquifer and was greatly affected by proximity to a ground water fed stream and whether the stream was tidally influenced. Away from the stream, the thickness of the fresh water lens decreased by about 2% from 1929 to 2050, whereas the fresh water lens thickness decreased by about 22% to 31% for the same period near the stream, depending on whether the stream was tidally influenced. The difference in the change in the fresh water/salt water interface position is controlled by the difference in the net decline in water levels relative to local sea level.

Effects of the South Delta Agricultural Barriers on Emigrating Juvenile Salmonids

California Department of Water Resources (DWR) | November 28th, 2018

The TBP is implemented in compliance with the terms and conditions of two NMFS Biological Opinions (BiOp) (NMFS 2008, 2009). To comply with the requirements of the NMFS

The TBP is implemented in compliance with the terms and conditions of two NMFS Biological Opinions (BiOp) (NMFS 2008, 2009). To comply with the requirements of the NMFS BiOps, a study of the effects of the three SDABs (i.e., ORTB, MRB, and GLCB) on emigrating (i.e., out-migrating) juvenile salmonids was conducted (2010–2011) and the results are reported in this document. There were four effects considered in this study: 1) survival of juvenile salmonids (Ŝ); 2) juvenile salmonid time-in-vicinity (TIV) of a barrier; 3) predation on juvenile salmonids; and 4) predatory fish density evaluations near the barriers before-, during-, and after- construction during each study year. For one barrier, the ORTB, two-dimensional (2D) acoustic fish tracks for juvenile salmonids were used to evaluate: 1) the rates of successful passage through the barrier; and 2) route selection through the barrier. In addition, utilizing the ORTB 2D fish tracks for both juvenile salmonids and predatory fish, a mixture model (Romine et al. 2014) approach was employed to determine the probability that a juvenile salmonid had been eaten by a predatory fish in the vicinity of the ORTB.

Effects of Urban Development on Stream Ecosystems in Nine Metropolitan Study Areas Across the United States

U.S. Geological Survey (USGS) | November 13th, 2012

Urban development is an important agent of environmental change in the United States. The urban footprint on the American landscape has expanded during a century and a ha

Urban development is an important agent of environmental change in the United States. The urban footprint on the American landscape has expanded during a century and a half of almost continuous development. Eighty percent of Americans now live in metropolitan areas, and the advantages and challenges of living in these developed areas—convenience, congestion, employment, pollution—are part of the day-to-day realities of most Americans. Nowhere are the environmental changes associated with urban development more evident than in urban streams. Contaminants, habitat destruction, and increasing streamflow flashiness resulting from urban development have been associated with the disruption of biological communities, particularly the loss of sensitive aquatic species. Every stream is connected downstream to larger water bodies, including rivers, reservoirs, and ultimately coastal waters. Inputs of chemical contaminants or sediments at any point along the stream can cause degradation downstream with adverse effects on biological communities and on economically valuable resources, such as fisheries and tourism. In response to general concerns about the degradation of urban streams, the U.S. Geological Survey (USGS) conducted a national-scale, scientific investigation of the effects of urban development on stream ecosystems. Nine metropolitan study areas of the United States were selected—Portland, Oregon; Salt Lake City, Utah; Birmingham, Alabama; Atlanta, Georgia; Raleigh, North Carolina; Boston, Massachusetts; Denver, Colorado; Dallas, Texas; and Milwaukee, Wisconsin. The studies were conducted in Salt Lake City, Birmingham, and Boston in 1999–2000; in Atlanta, Raleigh, and Denver in 2002–2003; and in Portland, Dallas, and Milwaukee in 2003–2004. The comprehensive investigation of all nine studies focused on three broad questions of interest to decision makers: 1. What are the primary effects of urban development on stream ecosystems? 2. How do the effects of urban development on stream ecosystems vary regionally across the country? 3. Which urban-related stressors are most closely linked to biological community degradation, and how can multiple stressors be managed to protect stream health as a watershed becomes increasingly urbanized? RELATED DOCUMENT: Strategies for Managing the Effects of Urban Development on Streams