Bed-Material Characteristics of the Sacramento–San Joaquin Delta, California, 2010–13

U.S. Geological Survey (USGS) | January 9th, 2017

The characteristics of bed material at selected sites within the Sacramento–San Joaquin Delta, California, during 2010–13 are described in a study conducted by the U.

The characteristics of bed material at selected sites within the Sacramento–San Joaquin Delta, California, during 2010–13 are described in a study conducted by the U.S. Geological Survey in cooperation with the Bureau of Reclamation. During 2010-13, six complete sets of samples were collected. Samples were initially collected at 30 sites; however, starting in 2012, samples were collected at 7 additional sites. These sites are generally collocated with an active streamgage. At all but one site, a separate bed-material sample was collected at three locations within the channel (left, right, and center). Bed-material samples were collected using either a US BMH–60 or a US BM–54 (for sites with higher stream velocity) cable-suspended, scoop sampler. Samples from each location were oven-dried and sieved. Bed material finer than 2 millimeters was subsampled using a sieving riffler and processed using a Beckman Coulter LS 13–320 laser diffraction particle-size analyzer. To determine the organic content of the bed material, the loss on ignition method was used for one subsample from each location. Particle-size distributions are presented as cumulative percent finer than a given size. Median and 90th-percentile particle size, and the percentage of subsample mass lost using the loss on ignition method for each sample are also presented in this report.

Benthic Invertebrate and Deposited Sediment TMDL Guidance for the Pajaro River Watershed

California State Water Resources Control Board (SWRCB) | March 1st, 2016

The Pajaro River and its tributaries are exposed to sediments from a variety of sources. To establish limits for regulating this pollutant, it is necessary to u

The Pajaro River and its tributaries are exposed to sediments from a variety of sources. To establish limits for regulating this pollutant, it is necessary to understand how and where deposition of sediments impact biological health. Benthic, or bottom-dwelling, invertebrates offer a direct way to assess the impacts of deposited sediment on the integrity of stream ecosystems. The channel bed is where sediments accumulate and persist, so benthic macroinvertebrates that live in this ha bitat provide a responsive indicator of the effect of these sediments. Previous criteria for bedded sediment fines in spawning gravels have been established for salmonids, but these may not be appropriate to all stream segments, are not typically measured in stream assessments, and are confounded by other factors limiting steelhead vitality. Instead, the effects of sediment cover can be evaluated using benthic macroinvertebrates (BMIs) as indicators of stream condition to assess any stream segment and can be related to the bioassessment and stream habitat surveys of the Surface Water Ambient Monitoring Program (SWAMP) . The approach taken in this study was to select 25 sites throughout the perennial Pajaro watershed and in the adjacent upper Coyote Creek watershed that represented a cross-section of land uses, above and below reservoirs (unregulated/regulated flows), and in varied geographic settings that would permit examining source area influences on sediment deposition. Rather than define conventional TMDL estimates for daily loads of sediment, a more relevant survey of the cover of deposited fine and sand (FS) sediments on the stream bed was used here to find the level at which BMIs lost integrity of species c omposition and diversity. BMI responses we re-examined at the reach scale (50-meter channel length ) and at local patch scales (30x3 0 cm) of varied FS sedim ent cover . The data were used to define target levels at which sediment impairs stream bed habitat quality. Reaches of varied sediment cover were compared to conditions at relatively undisturbed reference streams of the Central Coast region to evaluate sediment impacts. Significant loss of species diversity and altered community type occurred above a sediment cover range of 40% FS at both reach and local-patch scales. In a range of 20-40% FS , BMI diversity declined, showing incipient losses of biological integrity . Richness of mayfly, stonefly and caddisfly taxa richness (EPT) was used as an indicator of biological effects of sediment, and reduced diversity associated with sediment increase corresponded to declines below the criterion 10th percentile of reference site EPT found in other central coast streams . Because of multiple stressors, some streams may not achieve these sediment or EPT targets just by improving the local sediment condition . For example, streams that are regulated (below reservoirs) or in arid regions may be influenced by temperature, dissolved minerals and/or elevated pH , in addition to sediment . Rankings of streams surveyed were based either on sediment cover within the wetted stream width or the entire bankfull channel profile, accounting for both current habitat conditions and recent environmental exposure . Although the design of this study examined sediment deposition at different spatial scales and used a variety of sediment measures, the results are compatible with habitat and bioassessment surveys using standard SWAMP protocols. Only three to five of the 25 streams surveyed in the Pajaro region showed sediment and diversity levels indicating likely sediment deposition impacts. Results from this study can be used to identify streams where sediment degradation to biological integrity is likely (at >40% FS) , and those in a warning range (20-40% FS) that should be flagged for further assessment.

Beyond Watershed Planning: Engaging Communities to Improve Outcomes of the Safe Clean Water Program

Los Angeles Waterkeeper (LA Waterkeeper) | August 11th, 2026

In the eight years since Los Angeles voters approved Measure W, the LA County Flood Control District has successfully launched the Safe Clean Water Program (SCWP). The pr

In the eight years since Los Angeles voters approved Measure W, the LA County Flood Control District has successfully launched the Safe Clean Water Program (SCWP). The program collects approximately $280M every year and distributes those funds to support stormwater capture projects that can reduce flooding, improve regional water quality, recharge groundwater, and provide a variety of benefits for communities and wildlife. To date, the SCWP has funded 473 projects, studies, concepts, and program activities through its regional, municipal, and district programs.  The program takes an adaptive management approach to ensure funds are invested effectively and that supported projects deliver meaningful reductions in flood risk while providing appropriate treatment of local stormwater. This approach also ensures funds are leveraged to provide the most potential benefits for every dollar spent. As part of that effort, the SCWP developed a watershed planning process in 2024 with the goal of maximizing potential benefits in each of the county’s nine watersheds.  Los Angeles Waterkeeper secured funding to conduct five community workshops to further inform the watershed planning process moving forward. The purpose of these workshops was to ensure that individuals and organizations who are well informed about the on-the-ground needs and priorities of communities throughout LA County had the opportunity to provide input to the watershed plans. LA Waterkeeper partnered with community-based organizations in each of the areas where the workshops were held to invite priority participants, although all workshops were open to the public. 

Bifenthrin, a ubiquitous contaminant, impairs the development and behavior of the threatened Longfin Smelt during early life stages

American Chemical Society (ACS) | June 23rd, 2023

The Longfin Smelt (Spirinchus thaleichthys) population in the San Franscisco Bay/Sacramento-San Joaquin Delta (Bay-Delta) has declined to ∼1% of its pre-1980s abundance

The Longfin Smelt (Spirinchus thaleichthys) population in the San Franscisco Bay/Sacramento-San Joaquin Delta (Bay-Delta) has declined to ∼1% of its pre-1980s abundance and, as a result, is listed as threatened under the California Endangered Species Act. The reasons for this decline are multiple and complex, including the impacts of contaminants. Because the spawning and rearing seasons of Longfin Smelt coincide with the rainy season, during which concentrations of contaminants increase due to runoff, we hypothesized that early life stages may be particularly affected by those contaminants. Bifenthrin, a pyrethroid insecticide commonly used in agricultural and urban sectors, is of concern. Concentrations measured in the Bay-Delta have been shown to disrupt the behavior, development, and endocrine system of other fish species. The objective of the present work was to assess the impact of bifenthrin on the early developmental stages of Longfin Smelt. For this, embryos were exposed to 2, 10, 100, and 500 ng/L bifenthrin from fertilization to hatch, and larvae were exposed to 2, 10, and 100 ng/L bifenthrin from one day before to 3 days post-hatch. We assessed effects on size at hatch, yolk sac volume, locomotory behavior, and upper thermal susceptibility (via cardiac endpoints). Exposure to these environmentally relevant concentrations of bifenthrin did not significantly affect the cardiac function of larval Longfin Smelt; however, exposures altered their behavior and resulted in smaller hatchlings with reduced yolk sac volumes. This study shows that bifenthrin affects the fitness-determinant traits of Longfin Smelt early life stages and could contribute to the observed population decline.

Bioaccumulation of Pollutants in California Waters: A Review of Historic Data and Assessment of Impacts on Fishing and Aquatic Life

San Francisco Estuary Institute (SFEI) | October 24th, 2007

This report was written for the State Water Resources Control Board’s Surface Water Ambient Monitoring Program (SWAMP) as a step toward the development of an im

This report was written for the State Water Resources Control Board’s Surface Water Ambient Monitoring Program (SWAMP) as a step toward the development of an improved bioaccumulation monitoring program for California. The report provides a review of bioaccumulation monitoring data generated under three historic State Board programs (the Toxic Substances Monitoring Program, the State Mussel Watch Program, and the Coastal Fish Contamination Program) and other major bioaccumulation studies since 1970. Future monitoring will be guided by assessment questions developed for the SWAMP.  The objective of this report was to evaluate how well the historic data from the State Board programs and from other major monitoring efforts since 1970 address these questions. This exercise has provided a substantial amount of information about present and historical impacts of pollutant bioaccumulation on shing and aquatic life in California, and has also highlighted areas where improved sampling approaches can better address the assessment questions. Present concentrations of pollutants in many California water bodies are high enough to cause concern for possible effects on human health and to have a significant impact on the fishing beneficial use. Consumption advisories, 303(d) listings, and the bioaccumulation database as a whole provide three indices of the status of this impact. Consumption advisories exist for an increasing number of water bodies, but these represent only a fraction of the areas likely to need them. Lack of suitable data is a major impediment to developing advice for additional water bodies. A US E.P.A. evaluation of the 2002 303(d) List indicated that large portions of the state had not been assessed, especially rivers and coastline. Most of the lake area in the state (61%) had been assessed, and a relatively small percentage of the total area (6%) was classified as impaired. Assessment of lakes, however, has focused primarily on the largest lakes, leaving the vast majority of smaller lakes unsampled. Many of these small lakes are near population centers and are popular for shing. Bays and estuaries had been thoroughly assessed (98% of the area) and 93% of the total area was impaired. Evaluation of the most recent monitoring data (collected from 1998-2003) indicates that, for the locations sampled, 32% had low concentrations of pollutants, 42% had moderate concentrations, 18% had high concentrations, and 8% had very high concentrations (Figure 1). Concentrations in the low category are in a range where consumption is generally encouraged by the California Office of Environmental Health Hazard Assessment (OEHHA) (Klasing and Brodberg 2006). OEHHA is the agency responsible for managing health risks due to contaminated sport fish in California. Concentrations in the very high category are in a range where OEHHA discourages consumption (Klasing and Brodberg 2006). Lakes assigned to the moderate, high, or very high concentration categories were primarily affected by mercury, with PCBs also playing a lesser role.

Biological Condition of Non-Perennial Streams and Spring-Fed Oases in the Colorado River Basin Region

California State Water Resources Control Board (SWRCB) | August 22nd, 2014

The Colorado River Basin Regional Water Board conducted bioassessment sampling at high-quality (i.e., “reference”) streams in their region during 2013-2015. The purpo

The Colorado River Basin Regional Water Board conducted bioassessment sampling at high-quality (i.e., “reference”) streams in their region during 2013-2015. The purpose of the study was to characterize the biological condition of these streams, which had never been done before, and to expand ongoing research as to whether existing biological indices, developed primarily for perennial streams, apply in nonperennial streams. The latter are usually excluded from bioassessment surveys, but make up the majority of stream length in the most arid parts of the state like the Colorado River Basin, leaving stream condition assessments in such regions largely incomplete. The indices evaluated were the California Stream Condition Index (CSCI) based on benthic macroinvertebrates and the first to have statewide applicability in perennial streams, and the D18 and S2 indices for diatoms and soft algae, respectively, developed for use in perennial streams of southern coastal California. Sixteen sites were sampled during the 3-year period, and data loggers that measure water depth were deployed for 2 of the 3 years to characterize the hydrologic regime at each site. Most sites were nonperennial, but a few were spring-fed perennial oases. Fourteen of the sites passed formal reference screening criteria developed by statewide programs. The CSCI and S2 indices had generally good applicability in the region, with most samples from reference sites indicated either good or fair (i.e., non-degraded) biological condition. The mean CSCI score at regional reference sites was slightly lower than the statewide mean (i.e., 0.90 vs. 1.0, respectively), but the difference could be an artifact of a relatively small regional data set. The fact that CSCI and S2 performed as well as they did in a region, and in a set of stream types, largely excluded from their development indicates that the indices can be used in nonperennial streams (and spring-fed oases) in the Colorado River Basin as long as certain minimum flow conditions are met, such as sustained flow for several weeks prior to sampling and sufficient wetted width to employ existing protocols developed for perennial streams. By contrast, the D18 index did not perform well in the region. A majority of samples from reference sites indicated poor or very poor biological condition when condition thresholds based on statewide data sets were used, but even when more relaxed thresholds based on just south coast reference sites were applied, the number of reference sites in good or fair condition was still much lower than expected. This was not a result of regional reference sites being of low quality, but was most likely an artifact of applying the index to a set a stream types unintended for its use. Development of statewide algal indices is underway, which may improve the performance of diatom indices in the southern desert.

Biological opinion on the coordinated operations of the Central Valley Project (CVP) and State Water Project (SWP)

U.S. Fish and Wildlife Service (FWS) | December 15th, 2008

On May 16, 2008, the U.S. Bureau of Reclamation and the California Department of Water Resources asked the Service to initiate consultation on the Long-Term Operational C

On May 16, 2008, the U.S. Bureau of Reclamation and the California Department of Water Resources asked the Service to initiate consultation on the Long-Term Operational Criteria and Plan (OCAP) for coordination of the Central Valley Project and State Water Project, specifically concerning the delta smelt and its critical habitat. (See OCAP Legal Archives.) On December 15, 2008, the Fish & Wildlife Service issued a biological opinion (BO) on the Long-Term Operational Criteria and Plan (OCAP) for coordination of the Central Valley Project and State Water Project. The Service determined that the continued operation of these two water projects, as described in the plan, was likely to jeopardize the continued existence of the delta smelt and adversely modify its critical habitat. The inclusion by the Service of reasonable and prudent alternatives, and their acceptance by the water agencies, avoided jeopardy and adverse modification.

Biological sensitivities to high-resolution climate change projections in the California current marine ecosystem

Wiley | July 28th, 2022

Biology-based Stressor Thresholds

California State Water Resources Control Board (SWRCB) | October 1st, 2011

The objective of this memo is to describe how biological assessment data (such as those collected using Surface Water Ambient Monitoring Program (SWAMP) bioasse

The objective of this memo is to describe how biological assessment data (such as those collected using Surface Water Ambient Monitoring Program (SWAMP) bioassessment protocols) can be used to develop biologically-relevant stressor thresholds. This memo describes an objective approach for setting regulatory stressor thresholds based on the association between biological condition and stressor intensity gradients. While these relationships show a large amount of variability typical of biological data, there are clear thresholds that indicate levels below or above which stream health is maintained or degraded.

Bisphenols in San Francisco Bay: Wastewater, Stormwater, and Margin Sediment Monitoring

San Francisco Estuary Institute (SFEI) | October 28th, 2022

Bisphenols are a class of synthetic, mobile, endocrine-disrupting chemicals. Bisphenol A (BPA), the most well-studied bisphenol, is produced and used in vast quantities w

Bisphenols are a class of synthetic, mobile, endocrine-disrupting chemicals. Bisphenol A (BPA), the most well-studied bisphenol, is produced and used in vast quantities worldwide—especially in polycarbonate plastics and as a polymer additive. Recently, some manufacturers have begun using alternative bisphenol compounds, such as bisphenol F (BPF) and bisphenol S (BPS). These uses of bisphenols have led to widespread bisphenol detections in the environment and wildlife. The present study examined wastewater effluent in the San Francisco Bay Area and San Francisco Bay sediment samples for 17 bisphenols. The effluent samples were compared to available stormwater runoff data to better understand bisphenol transport, fate, and potential risks to wildlife.