Basin-scale responses of groundwater-resource quality to drought and recovery, San Joaquin Valley, California

Hydrological Processes (Wiley) | April 15th, 2024

Groundwater-resource quality is assumed to be less responsive to drought compared to that of surface water due to relatively long transit times of recharge to drinking-su

Groundwater-resource quality is assumed to be less responsive to drought compared to that of surface water due to relatively long transit times of recharge to drinking-supply wells. Here, we evidence dynamic perturbations in aquifer pressure dynamics during drought and subsequent recovery periods cause dramatic shifts in groundwater quality on a basin scale. We used a novel application of time-series clustering on annual nitrate anomalies at >450 public-supply wells (PSWs) across California's San Joaquin Valley during 2000–22 to group subpopulations of wells with similar water-quality responses to drought. Additionally, we statistically evaluated the direction and magnitude of multi-constituent water-quality changes across the San Joaquin Valley using a broader dataset of >3000 PSWs with data during two select hydrologic stress periods representing an extreme drought (2012–16) and subsequent recovery (2016–19). Results of time-series clustering and stress-period change analyses corroborate a predominant regional response to pumping stress characterized by increased concentrations of anthropogenic constituents (nitrate, total dissolved solids) and decreased concentrations of geogenic constituents (arsenic, fluoride), which largely reversed during recovery. Cluster analysis also identified a secondary, less commonly occurring group of PSWs where nitrate decreased during drought, but explanatory factor analysis was not able to discern hydrogeologic drivers for these two divergent response patterns. Long-term tracer data support the hypothesis that the predominant regional signal of nitrate increase during drought is caused by enhanced capture of modern-aged groundwater by PSWs during periods of pumping stress, which can drive rapid changes in water quality on seasonal and multiannual timescales. Pumping-induced migration of modern, oxic groundwater to depth during drought may affect geochemical conditions in deeper portions of regional aquifers controlling the mobility of geogenic contaminants over the long term.

Basis of Design Report - Species Conservation Habitat

California Department of Water Resources (DWR) | April 14th, 2014

The Species Conservation Habitat (SCH) project provides shallow water habitat to support fish and wildlife dependent upon the Salton Sea that is being lost due to

The Species Conservation Habitat (SCH) project provides shallow water habitat to support fish and wildlife dependent upon the Salton Sea that is being lost due to salinity increases and the declining water surface elevation. The Project is located at the southern end of the Salton Sea (Sea) in Imperial County, California. Through the environmental review process, a Preferred Alternative was selected that encompasses 3,770 acres on both sides of the New River. The Project would include water supplies, berms to contain the water, and various other support facilities. The early start construction of the project is to develop habitat consistent with the EIS/EIR preferred alternative that is scaled down to fit the level of implementation funding currently available. The design described in this report is for early start project (Project) of the SCH and is limited to the 640 acres located within the bay on the east side of the New River. This report provides a summary of the primary design features and considerations associated with the habitat development. A more detailed discussion of the background, purpose, goals, design elements, Preferred Alternative, and Project impacts can be found in the 2011 draft EIS/EIR.  

Bay Area Green Infrastructure Water Quality Synthesis

San Francisco Estuary Institute (SFEI) | June 1st, 2018

San Francisco Bay is impacted by the numerous urban pollutants that flow from the surrounding landscape during storm events. In San Francisco Bay, total maximum daily lo

San Francisco Bay is impacted by the numerous urban pollutants that flow from the surrounding landscape during storm events. In San Francisco Bay, total maximum daily load (TMDL) clean-up plans are in place for polychlorinated biphenyls (PCBs) and mercury (Hg) (Davis et al., 2007; Davis et al., 2012). As municipalities strive to reach regulatory targets, green infrastructure (GI) presents a promising solution for managing stormwater pollutants while achieving additional environmental and social benefits. However, remaining data gaps including the best design layout, media composition, and vegetation and submerged zone effects on performance can prevent local managers from accurately assessing water quality benefits provided by green infrastructure as well as the maintenance needs to sustain adequate performance.

Bay Delta Water Quality Control Plan (Bay Delta Plan)

California State Water Resources Control Board (SWRCB) | December 13th, 2006

"Bay Delta Plan" is short for the State Water Resources Control Board's (State Water Board) San Francisco Bay/Sacramento-San Joaquin Delta Estuary Water Quality Control P

"Bay Delta Plan" is short for the State Water Resources Control Board's (State Water Board) San Francisco Bay/Sacramento-San Joaquin Delta Estuary Water Quality Control Plan. The Bay-Delta Plan identifies the beneficial uses of the Bay-Delta, water quality objectives for the reasonable protection of those beneficial uses, and a program of implementation for achieving the objectives. The Bay-Delta Plan, when implemented, can determine the amount and timing of water entering and moving through the Delta. The State Water Board holds dual responsibilities of allocating surface water rights and protecting water quality. The State Water Board allocates water through an administrative system that is intended to maximize the beneficial uses of water while protecting the public trust, serving the public interest, and preventing the waste and unreasonable use or method of diversion of water. While most water quality control planning is done by the Regional Water Boards, the State Water Board has authority to adopt statewide water quality control plans. The State Water Board adopts the Bay-Delta Plan because of the Delta's importance as a major source of water supply for the state. The Bay-Delta Plan protects water quality in the region and includes water quality objectives to protect fish and wildlife beneficial uses through inflows to the Delta from the Sacramento and San Joaquin rivers and Delta outflows, in addition to objectives for salinity to protect agricultural beneficial uses. The State Water Resources Control Board (State Water Board) is in the process of a phased review and update of the 2006 Water Quality Control Plan for the San Francisco Bay/Sacramento-San Joaquin Delta Estuary (Bay-Delta) (referred to as the 2006 Bay-Delta Plan). To learn more about the Bay-Delta Plan, click here. In 2009, the State Water Board began the process of reviewing and likely revising the 2006 Bay Delta Plan.  At the time of the archiving of this document, that update process still continues.  For the latest information, click here to visit the State Water Resources Control Board page for the Bay-Delta Plan Update.. RELATED DOCUMENT: Water Rights Decision 1641, the document that implements the 1995 Bay Delta Plan and is still in force.

Bayesian nitrate source apportionment to individual groundwater wells in the Central Valley by use of elemental and isotopic tracers

American Geophysical Union (AGU) | July 31st, 2016

Groundwater quality is a concern in alluvial aquifers that underlie agricultural areas, such as in the San Joaquin Valley of California. Shallow domestic wells (less tha

Groundwater quality is a concern in alluvial aquifers that underlie agricultural areas, such as in the San Joaquin Valley of California. Shallow domestic wells (less than 150 m deep) in agricultural areas are often contaminated by nitrate. Agricultural and rural nitrate sources include dairy manure, synthetic fertilizers, and septic waste. Knowledge of the relative proportion that each of these sources contributes to nitrate concentration in individual wells can aid future regulatory and land management decisions. We show that nitrogen and oxygen isotopes of nitrate, boron isotopes, and iodine concentrations are a useful, novel combination of groundwater tracers to differentiate between manure, fertilizers, septic waste, and natural sources of nitrate. Furthermore, in this work, we develop a new Bayesian mixing model in which these isotopic and elemental tracers were used to estimate the probability distribution of the fractional contributions of manure, fertilizers, septic waste, and natural sources to the nitrate concentration found in an individual well. The approach was applied to 56 nitrate-impacted private domestic wells located in the San Joaquin Valley. Model analysis found that some domestic wells were clearly dominated by the manure source and suggests evidence for majority contributions from either the septic or fertilizer source for other wells. But, predictions of fractional contributions for septic and fertilizer sources were often of similar magnitude, perhaps because modeled uncertainty about the fraction of each was large. For validation of the Bayesian model, fractional estimates were compared to surrounding land use and estimated source contributions were broadly consistent with nearby land use types.

Beale Air Force Base Environmental Cleanup Program Issue 67

U.S. Air Force | October 31st, 2015

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.

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.