San Joaquin River

Assessment of Interim Flow Water-Quality Data of the San Joaquin River Restoration Program and Implications for Fishes, California, 2009–11

U.S. Geological Survey (USGS) | June 29th, 2015

After more than 50 years of extensive water diversion for urban and agriculture use, a major settlement was reached among the U.S. Departments of the Interior and Commerc

After more than 50 years of extensive water diversion for urban and agriculture use, a major settlement was reached among the U.S. Departments of the Interior and Commerce, the Natural Resources Defense Council, and the Friant Water Users Authority in an effort to restore the San Joaquin River. The settlement received Federal court approval in October 2006 and established the San Joaquin River Restoration Program, a multi-agency collaboration between State and Federal agencies to restore and maintain fish populations, including Chinook salmon, in the main stem of the river between Friant Dam and the confluence with the Merced River. This is to be done while avoiding or minimizing adverse water supply effects to all of the Friant Division contractors that could result from restoration flows required by the settlement. The settlement stipulates that water- and sediment-quality data be collected to help assess the restoration goals. This report summarizes and evaluates water-quality data collected in the main stem of the San Joaquin River between Friant Dam and the Merced River by the U.S. Bureau of Reclamation for the San Joaquin River Restoration Program during 2009–11. This summary and assessment consider sampling frequency for adequate characterization of variability, sampling locations for sufficient characterization of the San Joaquin River Restoration Program restoration reach, sampling methods for appropriate media (water and sediment), and constituent reporting limits. After reviewing the water- and sediment-quality results for the San Joaquin River Restoration Program, several suggestions were made to the Fisheries Management Work Group, a division of the San Joaquin River Restoration Program that focuses solely on the reintroduction strategies and health of salmon and other native fishes in the river. Water-quality results for lead and total organic carbon exceeded the Surface Water Ambient Monitoring Program Basin Plan Objectives for the San Joaquin Basin, and results for copper exceeded the U.S. Environmental Protection Agency Office of Pesticide Programs’ aquatic-life chronic and acute benchmarks for invertebrates. One sediment sample contained detections of pyrethroid pesticides bifenthrin, lambda-cyhalothrin, and total permethrin at concentrations above published chronic toxicity thresholds.

Assessment of Nutrient Status and Trends in the Delta in 2001–2016: Effects of drought on ambient concentrations and trends

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

Nutrients and the effects of nutrients on water quality in the Sacramento-San Joaquin Delta is a priority focus area for the Delta Regional Monitoring Program (Delta RMP)

Nutrients and the effects of nutrients on water quality in the Sacramento-San Joaquin Delta is a priority focus area for the Delta Regional Monitoring Program (Delta RMP). The Program’s first assessment question regarding nutrients is: “How do concentrations of nutrients (and nutrient-associated parameters) vary spatially and temporally?” In this analysis, we confirmed previously reported declining trends in the San Joaquin River for nutrient concentrations at Vernalis and chlorophyll-a concentrations at Buckley Cove and Disappointment Slough. A slight increasing trend for dissolved oxygen at Buckley Cove was also detected which could be confirmation that management actions for the San Joaquin River Dissolved Control Program are having the desired effect. Finally, at stations in Suisun Bay, the Confluence region, and Franks Tract, chlorophyll-a showed modest increasing trends, which were not evident in previous analyses. The new analyses presented in this report and the findings from earlier reports constitute encouraging early progress toward answering the Delta RMP’s assessment questions. Specifically, due to the existence of long-term data sets and synthesis efforts, spatial and temporal trends in the concentrations of nutrients and nutrient-related parameters are reasonably well understood and so are the magnitudes of the most important sources of nutrients from outside the Delta. However, additional synthesis work could be done to understand the factors behind these trends. Large knowledge gaps remain about nutrient sinks, sources, and processes within the Delta. The mechanistic, water quality-hydrodynamic models being developed for the Delta may be able to address these questions in the future.

Assumptions and Estimates for California Water Plan Update 2023 (Draft)

California Department of Water Resources (DWR) | October 14th, 2022

The draft Assumptions and Estimates for California Water Plan Update 2023 (draft A&E Report) describes key assumptions and estimates, data and data sources; improvements

The draft Assumptions and Estimates for California Water Plan Update 2023 (draft A&E Report) describes key assumptions and estimates, data and data sources; improvements to analytical tools, methods, and approaches; and the supporting documents and companion State plans being used to prepare California Water Plan Update 2023 (Update 2023), State government’s strategic plan for managing and developing water resources for sustainability and resilience. The draft A&E Report cites the statutory requirements for the California Water Plan (Water Plan), key legislative and policy drivers, assumptions, and estimates related to water data portfolios, future scenarios, water accounting, watershed resilience planning, and equity in water resource management. Also discussed are resource management strategies, the alignment of integrated watershed programs and plans, and integration and alignment of State plans.

Authority and Effectiveness of the State Water Resources Control Board

Delta Vision Blue Ribbon Task Force (Delta Vision) | July 1st, 2008

This report addresses issues related to the effectiveness of the California State Water Resources Control Board (“State Board” or “Board”) in carrying out its rol

This report addresses issues related to the effectiveness of the California State Water Resources Control Board (“State Board” or “Board”) in carrying out its roles and responsibilities, with particular reference to the Sacramento-San Joaquin San Francisco Bay-Delta (“Delta”). Section 1 presents an overview and evaluation of the authority and responsibility of the State Board. Section 2 describes actions of the State Board over many years in connection with the Delta, and in summary form, the Mono Lake basin and the Yuba River. Based on the preceding sections, Section 3 evaluates the effectiveness of the Board with particular reference to the Delta and sets forth some observations related to the Board’s authority and effectiveness.

Availability of high-magnitude streamflow for groundwater banking in the Central Valley, California

Environmental Research Letters (IOP) | July 31st, 2017

California’s climate is characterized by the largest precipitation and streamflow variability observed within the conterminous US This, combined with chronic gr

California’s climate is characterized by the largest precipitation and streamflow variability observed within the conterminous US This, combined with chronic groundwater overdraft of 0.6–3.5 km3 yr 1, creates the need to identify additional surface water sources available for groundwater recharge using methods such as agricultural groundwater banking, aquifer storage and recovery, and spreading basins. High-magnitude streamflow, i.e. flow above the 90th percentile, that exceeds environmental flow requirements and current surface water allocations under California water rights, could be a viable source of surface water for groundwater banking. Here, we present a comprehensive analysis of the magnitude, frequency, duration and timing of high-magnitude streamflow (HMF) for 93 stream gauges covering the Sacramento, San Joaquin and Tulare basins in California. The results show that in an average year with HMF approximately 3.2 km3 of high-magnitude flow is exported from the entire Central Valley to the Sacramento-San Joaquin Delta often at times when environmental flow requirements of the Delta and major rivers are exceeded. High-magnitude flow occurs, on average, during 7 and 4.7 out of 10 years in the Sacramento River and the San Joaquin-Tulare Basins, respectively, from just a few storm events (5–7 1-day peak events) lasting for 25–30 days between November and April. The results suggest that there is sufficient unmanaged surface water physically available to mitigate long-term groundwater overdraft in the Central Valley.

Background and Recent History of Water Transfers in California

California Department of Water Resources (DWR) | July 1st, 2015

The purpose of this paper is to provide a basic understanding of water transfers in California with an emphasis on transfers that move water through the Sacramento-

The purpose of this paper is to provide a basic understanding of water transfers in California with an emphasis on transfers that move water through the Sacramento-San Joaquin Delta (Delta). This paper provides an overview of various types of water transfers, their recent history, and the regulatory setting that governs transfers. In its 1976 report, the Governor’s Commission on Water Rights recognized the importance of water transfers to the future of California’s water supply and made recommendations regarding the need for specific changes to the Water Code to facilitate the transfer of water. Many of these changes were accomplished in the following years and are reflected in the discussions below. Water transfers involve a change in the place of water use, from the water’s historic point of diversion and use, to a new location either within or outside the watershed of origin. Water may be transferred from one user to another for a variety of purposes, including agricultural, municipal and industrial uses. It may also be transferred for environmental purposes such as in-stream flow augmentation and wildlife refuges. Water transfers and exchanges can be temporary (up to one year) or long-term (more than one year, but not permanent) or permanent. Water transfers can be an effective water management tool providing much-needed flexibility in the allocation and use of water in California. Transfers in California are primarily executed to meet dry-year demands rather than to obtain a primary water supply for either agricultural or municipal development. Transfers are particularly useful for meeting critical needs during drought periods. Transfers, however, must be carried out in a responsible manner in order to assure that they do not result in adverse impacts to other water users or unreasonable effects to the environment.

Base of fresh ground water (approximately 3,000 micromhos) in the San Joaquin Valley, California

U.S. Geological Survey (USGS) | June 30th, 1971

Widespread pumping of groundwater in the San Joaquin Valley began about 1900, and since 1940 pumpage has increased at an accelerated rate. In response to the heavy withdr

Widespread pumping of groundwater in the San Joaquin Valley began about 1900, and since 1940 pumpage has increased at an accelerated rate. In response to the heavy withdrawal of groundwater, water levels have declined rapidly beneath extensive areas of the valley. Consequently, it becomes necessary to delineate the base of fresh groundwater so that changes in thickness of the fresh-water zone can be monitored, and limited depths of water wells can be determined. In turn, those data will be useful in determining favorable areas for groundwater storage, and areas and depths for waste-water disposal wells. Because other agencies and the U.S. Geological Survey have collected a vast amount of well log and other data, most of the information in this report was assembled from existing files. However, for areas where data were scanty, a few hundred additional electrical logs were collected to supplement the available information.

Base of fresh water, groundwater salinity, and well distribution across California

National Academy of Sciences (NAS) | December 9th, 2020

The depth at which groundwaters transition from fresh to more saline—the “base of fresh water”—is frequently used to determine the stringency and types of measure

The depth at which groundwaters transition from fresh to more saline—the “base of fresh water”—is frequently used to determine the stringency and types of measures put in place to manage groundwater and protect it from contamination. Therefore, it is important to understand salinity distributions and compare defined bases of fresh water with salinity distributions and groundwater well depths. Here we analyze two distinct datasets: 1) a large set of total dissolved solids concentration (TDS) measurements (n = 216,754) and 2) groundwater well locations and depths (n = 399,454) across California. We find that 19 to 56% of the groundwater TDS measurements made at depths deeper than defined bases of fresh water pump fresh groundwater (TDS < 2,000 mg/L). Because fresh groundwater is found at depths deeper than the base of fresh water, current policies informed by base of fresh water assessments may not be managing and protecting large volumes of deep fresh groundwater. Furthermore, we find that nearly 4% of existing groundwater wells penetrate defined bases of fresh water, and nearly 16% of wells overlie it by no more than 100 m, evidencing widespread encroachment on the base of fresh water by groundwater users. Consequently, our analysis suggests that groundwater sustainability in California may be poorly safeguarded in some places and that the base-of-fresh-water concept needs to be reconsidered as a means to define and manage groundwater.

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.

Battling the Inland Sea

University of California Press | July 1st, 1998