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.

Bioanalytical and chemical-specific screening of contaminants of concern in three California (USA) watersheds

Heliyon (Elsevier) | May 5th, 2022

To broaden the scope of contaminants monitored in human-impacted riverine systems, water, sediment, and treated wastewater effluent were analyzed using receptor-based cel

To broaden the scope of contaminants monitored in human-impacted riverine systems, water, sediment, and treated wastewater effluent were analyzed using receptor-based cell assays that provide an integrated response to chemicals based on their mode of biological activity. Samples were collected from three California (USA) watersheds with varying degrees of urbanization and discharge from municipal wastewater treatment plants (WWTPs). To complement cell assay results, samples were also analyzed for a suite of contaminants of emerging concern (CECs) using gas and liquid chromatography-mass spectrometry (GC- and LC-MS/MS). For most water and sediment samples, bioassay equivalent concentrations for estrogen and glucocorticoid receptor assays (ER- and GR-BEQs, respectively) were near or below reporting limits. Measured CEC concentrations compared to monitoring trigger values established by a science advisory panel indicated minimal to moderate concern in water but suggested that select pesticides (pyrethroids and fipronil) had accumulated to levels of greater concern in river sediments. Integrating robust, standardized bioanalytical tools such as the ER and GR assays utilized in this study into existing chemical-specific monitoring and assessment efforts will enhance future CEC monitoring efforts in impacted riverine systems and coastal watersheds.

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.

Calibration of the Multivariate AZTI Marine Biotic Index (M-AMBI) for Potential Inclusion into California Sediment Quality Objective Assessments in San Francisco Bay

San Francisco Estuary Institute (SFEI) | April 30th, 2019

Benthic infauna are the most common faunal assemblage used to assess habitat quality across the globe as they demonstrate relatively predictable community-scale changes i

Benthic infauna are the most common faunal assemblage used to assess habitat quality across the globe as they demonstrate relatively predictable community-scale changes in both structure and function when exposed to stress. Due to these characteristics, benthic infauna are used as one of three lines of evidence in California’s Sediment Quality Objectives (CASQO) to assess the impact of toxic chemicals to biotic resources in the State’s enclosed bays and estuaries. The changes in benthic community composition related to disturbance are quantified using benthic assessment indices. 

Can restoring water and sediment fluxes across a mega-dam cascade alleviate a sinking river delta?

American Association for the Advancement of Science (AAAS) | May 1st, 2024

Causes of Variability in Suspended‐Sand Concentration Evaluated Using Measurements in the Colorado River in Grand Canyon

American Geophysical Union (AGU) | July 29th, 2020

Rivers commonly exhibit substantial variability in suspended‐sand concentration, even at constant water discharge. Here we derive an approach for evaluating how m

Rivers commonly exhibit substantial variability in suspended‐sand concentration, even at constant water discharge. Here we derive an approach for evaluating how much of this variability arises from mean bed‐sand grain size. We apply this approach to the Colorado River in Grand Canyon, where discharge‐independent concentration of suspended sand varies by more than a factor of 23 (N = 1.4 × 106). Theory predicts that where concentration is controlled by bed‐sand grain size, concentration and grain size in suspension will be inversely correlated (i.e., coarsening of the bed causes suspended sand to become coarser in grain size and lower in concentration). Although the observed correlation is negative, riverbed grain size accounts for only 40% of the variability in concentration. The residuals vary by an order of magnitude; they arise from other processes, such as changes in topography or distribution of sand that cause shear stress to change at constant discharge, changes in the fine tail of bed‐sand grain sizes or changing bedforms. Both bed sand and the other factors influence concentration for durations from less than 1 day to several years. Predictions of concentration based on bed‐sand grain size (N = 4 × 104) are less accurate than predictions based on suspended‐sand grain size, probably because suspended sand is a natural integrator of sand‐transporting processes, giving more weight to those areas of the bed that exchange more sand with the flow. Although the causes of variability vary from one river to another, the approach illustrated here is applicable to any river in which concentration varies at constant water discharge.

Characterization of Sediment Contamination in Central Bay Margin Areas

San Francisco Estuary Institute (SFEI) | July 2nd, 2018

The Bay margins (i.e., mudflats and adjacent shallow areas of the Bay) are important habitats where there is high potential for wildlife to be exposed to contaminants. H

The Bay margins (i.e., mudflats and adjacent shallow areas of the Bay) are important habitats where there is high potential for wildlife to be exposed to contaminants. However, these areas are not routinely sampled due to logistical considerations. In 2015, the Regional Monitoring Program for Water Quality in San Francisco Bay (RMP) conducted a survey of margin areas in Central Bay to determine ambient concentrations of contaminants in sediment in these areas. The results generally confirmed the current conceptual model expectation that the margin sediments are often more contaminated that those in the subtidal open bay, with PCBs showing the largest differences. These differences between Central Bay margins and open water areas are likely the largest to be found in San Francisco Bay, as margins in other bay segments generally account for more of the total area and the adjacent land use is less heavily industrial. The ambient data provide a useful baseline context against which the severity of contamination at specific sites can be compared. The baseline data will also be useful in setting targets and tracking improvements in watershed loads and their nearfield receiving waters, or for appropriate re-use or disposal of dredged sediment. These spatially unbiased data can also improve estimates of mean concentrations and contaminant inventories in margins. For example, based on data from this study, contamination in the margin areas accounts for ~20% of PCBs in Central Bay which is disproportionately high compared to the margin area (5% of Central Bay). Given a large inventory of contaminants in the open bay compared to annual loads, changes may be difficult to see at the bay scale in the short- and mid-term. However, with margins’ smaller inventories and greater proximity to likely sources, improvements in margin sediments may be easier to observe. This ambient sampling effort also identified or verified one expected area of very high PCB concentrations which had not been previously measured. However, the randomized monitoring design used for the Central Bay study was not ideal for identifying “hot spots”. Future studies with a goal of detecting hot spots should use deterministic sampling designs.

Characterization of Sediment Contamination in South Bay Margin Areas

San Francisco Estuary Institute (SFEI) | November 15th, 2019

The Bay margins (i.e., mudflats and adjacent shallow areas of the Bay) are important habitats where there is high potential for wildlife to be exposed to contaminants. Ho

The Bay margins (i.e., mudflats and adjacent shallow areas of the Bay) are important habitats where there is high potential for wildlife to be exposed to contaminants. However, until recently, these areas had not been routinely sampled by the Regional Monitoring Program for Water Quality in San Francisco Bay (RMP) due to logistical considerations. In 2015, the RMP conducted a spatially-distributed characterization of surface sediment contamination and ancillary characteristics within the RMP-defined Central San Francisco Bay margin areas. This was repeated in 2017 within South Bay, which for this report refers to the area collectively encompassing Upper South Bay (usually just called the “South Bay” segment in the Bay RMP, “Upper” added here to distinguish from the combined area), Lower South Bay, and “Extreme” Lower South Bay (previously named “Southern Sloughs”) margin areas.  Findings from the 2015 survey of margin areas in Central Bay (Yee et al., 2017) showed contamination in the margin areas accounted for 20% of the PCB mass in Central Bay, which is disproportionately high compared to margin area (5% of Central Bay). Central Bay watersheds contains many of the oldest and most industrialized urban environments within the Bay Area. There was a significant difference in mean contaminant concentrations in sediment from margins and nearby open water areas. In contrast, for South Bay, margins are more proximate to open water areas and represent a greater percentage of the overall Bay surface area. Therefore, as hypothesized, in the South Bay more uniform distributions were found, likely in part due to these physical factors. Average concentrations in South Bay margins were lower than in Central Bay margins, which was also hypothesized, because South Bay watersheds contain more recent industrial development and relatively less older industrial areas as a percentage of total area (~2% vs 5% for Central Bay watersheds). Although combined loads of PCBs from the South Bay watersheds are about 40% higher than from Central Bay areas, their total area is over 5 times larger, and their total runoff volume is more than double.  Ambient margins data in South Bay provide a context against which the severity of contamination at specific sites can be compared. The baseline data could also be useful in setting targets and tracking improvements in watershed loads and their nearfield receiving waters, or for appropriate assessment of re-use or disposal of dredged sediment. These spatially distributed data also provide improved estimates of mean concentrations and contaminant inventories in margins. Based on data from this study, contamination in the margin areas accounts for 35% of PCB mass in the upper 15 cm of surface sediments in South Bay, which is approximately proportional to the relative area of the margin (34% of the region). In contrast, margins only contain 30% of the mercury mass in South Bay, somewhat less than their proportional area.  Given the large inventory of contaminants in the open Bay compared to annual loads, changes may be difficult to see in the open Bay in the short- and mid-term. However, due to their smaller inventories and closer proximity to likely sources and loading pathways, improvements in margin sediments may potentially be detected more easily or sooner as loads are reduced, even if South Bay margins are better connected and more similar in concentrations to adjacent open water areas than in Central Bay. 

Characterizing changes in streamflow and sediment supply in the Sacramento River basin, California, using hydrological simulation program

Water, Multidisciplinary Digital Publishing Institute (MDPI) | September 30th, 2016

A daily watershed model of the Sacramento River Basin of northern California was developed to simulate streamflow and suspended sediment transport to the San Francisco B

A daily watershed model of the Sacramento River Basin of northern California was developed to simulate streamflow and suspended sediment transport to the San Francisco Bay-Delta. To compensate for sparse data, a unique combination of model inputs was developed, including meteorological variables, potential evapotranspiration, and parameters defining hydraulic geometry. A slight decreasing trend of sediment loads and concentrations was statistically significant in the lowest 50% of flows, supporting the observed historical sediment decline. Historical changes in climate, including seasonality and decline of snowpack, contribute to changes in streamflow, and are a significant component describing the mechanisms responsible for the decline in sediment. Several wet and dry hypothetical climate change scenarios with temperature changes of 1.5 C and 4.5 C were applied to the base historical conditions to assess the model sensitivity of streamflow and sediment to changes in climate. Of the scenarios evaluated, sediment discharge for the Sacramento River Basin increased the most with increased storm magnitude and frequency and decreased the most with increases in air temperature, regardless of changes in precipitation. The model will be used to develop projections of potential hydrologic and sediment trends to the Bay-Delta in response to potential future climate scenarios, which will help assess the hydrological and ecological health of the Bay-Delta into the next century.

Clay Mineralogy of Pleistocene Lake Tecopa

U.S. Geological Survey (USGS) | July 1st, 1979