San Joaquin River

Salt Water Problem: San Francisco Bay and Delta of Sacramento and San Joaquin Rivers

Association of Industrial Water Users of Contra Costa and Solano Counties | April 12th, 1928

PENETRATION OF SALT WATER IN UPPER BAY AND LOWER RIVER REGiON Under natural conditions, Carquinez Straits marked, approximately, the boundary between salt and fresh

PENETRATION OF SALT WATER IN UPPER BAY AND LOWER RIVER REGiON Under natural conditions, Carquinez Straits marked, approximately, the boundary between salt and fresh water in the upper San Francisco Bay and delta region of the two tributary rivers-the Sacramento and San Joaquin. Ordinarily salt water was present below the straits and fresh water was present above. Native vegetation in the tide marshes was predominantly of salt water types around San Pablo Bay and of fresh water types around Suisun Bay. In tidal waters, into which run fresh water streams of variable flow, there is an ebb and flow of salt water and the zone of mixing will move up and down stream as the fresh water flow increases and decreases. For short intervals in late summer of years of minimum flow, salt water penetrated the lower river and delta region, and in wet seasons the upper bay was fresh, part of the time, to the Golden Gate. This variation in quality of water was not, however, of sufficient duration to affect the characteristic vegetation growth of the regions on each side of the straits, nor to change the designation of Suisun Bay as ordinarily a fresh water body and San Francisco Bay as salt water. The works of man have changed conditions in many ways. The most important changes have been brought about gradualJy,-so slowly as to be hardly noticeable. The dry season of 1918,-when large summer diversions for irrigation in the Sacramento Valley resulted in the sudden penetration of salt water farther upstream than ever known before, at such an early period in summer first brought the salt water problem to public notice. The slow effects of increasing diversions in previous years had escaped notice, but were brought prominently to the attention of the inhabitants of the upper bay and delta regions in this year. Since 1918, the dry years of 1920, 1924- and 1926 have more convincingly demonstrated the importance of the salt water problem. An accurate picture of natural conditions is not possible, because no records have been collected on which such a picture can be based, but very close approximations can be made. The log of the distance traveled by the water barge of the California Hawaiian Sugar Company in going upstream to obtain fresh water has been kept since 1908. These figures give the means of determining approximately the conditions during that period. In 1908 irrigation had been extensively developed in both valleys and conditions then were not natural. For an estimate of earlier conditions we must go to the stream flow records of the tributary streams before important diversions are taken out. It is the practice of the Sugar Company to send the barge upstream until water of approximately 50 to 70 parts per million chlorine is reached. The crew of the barge are equipped with apparatus by which water is analyzed until this degree of purity is reached. Since trips are made nearly every day during the summer months, the record is a very good indication of the point reached by salt water. A summary of the complete records shows the fluctuation of the line between fresh and salt water. Records of the Sugar Company arc attached. (Table 1.) The Sugar Company requires water of great purity. For irrigation, domestic or ordinary industrial uses, water of a lesser degree of purity may be used. A comparison of the point where the Sugar Company's barge is filled with the point where the remaining uses could be satisfied, indicates that from five to ten miles downstream from the place where the barge turns, water could be obtained satisfactory for domestic supply. Making an allowance of 7 1/2 miles in the average records, we find that an average flow of 5,000 second feet in both streams will maintain fresh water at Collinsville; 7,000 second feet will maintain fresh water at the San Francisco-Sacramento ferry. If we sum up the flow of the important tributaries of the Sacramento and San Joaquin rivers at the points where these streams leave the mountains and assume that this flow under natural conditions would have reached the head of the Suisun Bay we will find that at no time in the past ten years would the average monthly flow have been Jess than 5,100 second feet. It is probable, should all streams be running in a natural way, that salt water would have penetrated no farther in this extremely dry period than Antioch, and then only for a few days at a time. It is not possible to make a more detailed study of this condition without making a number of assumptions as to speed of flow from the gaging stations to the head of the bay, and there is little accurate information on which the assumptions may be made. The definite statement that salt water under natural conditions did not penetrate higher upstream than the mouth of the river, except in the driest years and then only for a few days at a time, is warranted. (See Table 2 for monthly flow of tributary streams.) At present salt water reaches Antioch every year, in two-thirds of the years running further upstream. It is to be expected that it will continue to do so in future, even in years of greatest runoff. In other words, the penetration of salt water has become a permanent phenomenon in the lower river region.

Sampling for Per- and Polyfluoroalkyl Substances (PFAS) by the Groundwater Ambient Monitoring and Assessment Priority Basin Project

Publisher not available | May 25th, 2021

San Andreas Fault Stress Change Due To Groundwater Withdrawal in California's Central Valley, 1860-2010

American Geophysical Union (AGU) | December 28th, 2021

We investigate the spatial and temporal effects of groundwater removal in California's Central Valley on ground surface deformation and on stress changes on the nearby ce

We investigate the spatial and temporal effects of groundwater removal in California's Central Valley on ground surface deformation and on stress changes on the nearby central San Andreas fault (CSAF). In particular, we focus on two outstanding questions: (a) What are the spatial distributions of Coulomb failure stress (ΔCFS) on the CSAF? (b) What are the effects of viscoelasticity on uplift and ΔCSF over time? We focus on the well studied 2006–2010 drought, estimating the change in groundwater storage and the resulting uplift and stress change through a numerical model for the Earth. Viscoelastic effects are examined through an estimate of historical groundwater change from 1860-1961 and a hydrological model from 1961-2003 added to the 2006–2010 drought estimates. Here we find that lower crust or upper mantle viscosity variations enhance uplift and stress changes and that CSAF stress changes may accumulate with time, especially with droughts and groundwater consumption.

San Francisco Bay California Toxics Rule Priority Pollutant Ambient Water Monitoring Report

San Francisco Estuary Institute (SFEI) | February 1st, 2017

In 2000, the USEPA published Water Quality Standards; Establishment of Numeric Objectives for Priority Toxic Pollutants for the State of California, commonly known as t

In 2000, the USEPA published Water Quality Standards; Establishment of Numeric Objectives for Priority Toxic Pollutants for the State of California, commonly known as the California Toxics Rule (CTR), which established numeric water quality standards for 126 priority pollutants. Under the Policy for Implementation of Toxics Standards for Inland Surface Waters, Enclosed Bays, and Estuaries of California (also known as the State Implementation Policy, SIP) the San Francisco Bay Regional Water Quality Control Board (SFBRWQCB) is required to establish water quality-based effluent limitations in order to achieve priority pollutant standards. For the purposes of this document “water quality criteria” (WQCs) will be used to refer both to the CTR established numeric criteria for 126 priority pollutants as well as to numeric objectives for 12 of these priority pollutants and tributyltin previously established in the San Francisco Bay Water Quality Control Plan (Basin Plan) and/or the National Toxics Rule. A number of these pollutants previously were or continue to be regularly monitored as part of the Regional Monitoring Program Status and Trends (RMP S&T). The priority pollutants not routinely included in RMP S&T were previously monitored in wet and dry season ambient water sampling in 2002 and 2003. Results of that effort are detailed in a previously issued : Most of the priority pollutants were not detected in that study, or detected at concentrations below their WQC. Among the pollutants that were detected, a number of them were also found at similar concentrations in lab blanks, suggesting they might not have been present (or at least were at lower concentrations) in the ambient environment. Since over a decade had passed since that previous monitoring effort, the RMP embarked on an effort to repeat measurement of these seldom analyzed (non- S&T) contaminants, to ensure conditions have not changed appreciably to present greater risk for any of them.

San Francisco Bay: A Freshwater Starved Estuary

Bay Institute | September 1st, 2016

How Reducing Flows Harms the Ecosystems of San Francisco Bay and Coastal Waters The Bay Institute’s major new study, San Francisco Bay: The Freshwater – Starved Estu

How Reducing Flows Harms the Ecosystems of San Francisco Bay and Coastal Waters The Bay Institute’s major new study, San Francisco Bay: The Freshwater – Starved Estuary, documents how the ecological health of San Francisco Bay and the nearby ocean is at high risk because large-scale water diversion in the Bay’s watershed severely limits the amount of fresh water that reaches the Bay and alters the timing of that flow. Inflow to the Bay from its Central Valley watershed now averages less than half of what it would be without diversions; in some years just one-third of the runoff makes it to the Bay. The result is a nearly permanent drought for the Bay’s fish, wildlife, and their habitats. This radical alteration creates severe consequences for the Bay and marine ecosystems – and Bay Area residents pay the price. The study shows how unsustainable diversion of the Bay’s freshwater inflow: Dramatically cuts production of fish and shrimp that are the food source for marine mammals, like Orca Whales, and birds; Allows pollutants to accumulate to dangerous levels and encourages blooms of toxic algae; Reduces sediment supply to Bay Area wetlands and beaches; Makes it easier for undesirable non-native species to successfully invade the Bay Estuary. The San Francisco Bay Estuary is created by the mixing of fresh water from the Central Valley’s rivers with salt water from the Pacific Ocean. Dramatically reducing the inflow of fresh water generates cascading effects in the Bay’s watershed, the Bay itself, and coastal ocean waters. The report’s major findings include: On average, since 1975 more than half (53%) of runoff from the Central Valley watershed has been diverted, stored, or exported before it can reach the Bay – and in many years two-thirds or more of the Bay’s inflow is captured; As a result of intensive water diversions, the Bay experiences catastrophically dry years almost half the time (only one “supercritically dry” year occurred naturally between 1975-2014, but the Bay experienced nineteen supercritical years during that period); Numerous unrelated fish species – from sharks to salmon, from sturgeon to smelt – show strong positive correlations with Bay Inflow; many of these species are now endangered, and even commercially viable fisheries are in decline; Predators that feed on flow-dependent fish and shrimp are feeling the pinch – for example, dwindling supplies of Central Valley Chinook salmon may restrict the recovery of the local Orca whale population; Blooms of toxic “algae” (cyanobacteria) are becoming more frequent, and other pollutants are becoming more concentrated, as a result of reductions in freshwater flows from the Bay’s watershed; Bay Area beaches and tidal wetlands are deprived of sediment that was once transported by high river flows. The study reports that local businesses are likely to suffer from the Bay’s continued decline, including those related to commercial fishing and tourism. As our Bay, beaches, wetlands, and fish and wildlife populations deteriorate, the quality of life for many Bay Area residents will also be severely – and perhaps permanently – damaged. The study identifies four important approaches to improving Bay inflows: Update the State’s 21 year old water quality standards for the Bay Estuary to ensure adequate inflow Require all those who divert water destined for the Bay, not just a subset, to contribute their fair share of fresh water to support benefits enjoyed by all Californians Invest in local water supplies around the state including conservation, and recycling, that can generate millions of acre-feet of water and reduce reliance on water diverted from the Estuary and its watershed Coordinate management of flows with wetland and beach restoration to more effectively protect shorelines The study was prepared for the San Francisco Estuary Partnership, a coalition of resource agencies, non-profits, citizens, and scientists working to protect, restore, and enhance water quality and fish and wildlife habitat in and around the San Francisco Bay Delta Estuary, which also provided the majority of funding for the project.

San Francisco Estuary Blueprint 2022

San Francisco Estuary Partnership (SFEP) | September 8th, 2022

In the past few years, the San Francisco Estuary region has confronted epic wildfires, historic rainfall intensity and flooding, and chronic drought. The whiplash of thes

In the past few years, the San Francisco Estuary region has confronted epic wildfires, historic rainfall intensity and flooding, and chronic drought. The whiplash of these events has confirmed that climate change has already begun to impact human and wildlife communities from Sacramento to San Francisco, and beyond. Furthermore, a global COVID-19 pandemic has disrupted regional planning and project implementation everywhere, presenting new challenges to traditional processes and creating an unfamiliar working landscape for resource managers. Finally, the pervasive, horrific violence against Black, Brown, and Asian and Asian-American people has amplified long-term calls for racial justice, galvanizing new commitments to address historic and present inequity through every thread of our social fabric. These events have set the context for the multi-stakeholder process that updates the San Francisco Estuary Blueprint.

San Francisco Estuary Blueprint 2022 (Comprehensive Conservation and Management Plan for the San Francisco Estuary)

San Francisco Estuary Partnership (SFEP) | March 16th, 2022

Click here for the definition of a Comprehensive Conservation and Management Plan)

Click here for the definition of a Comprehensive Conservation and Management Plan)

San Joaquin Basin Flood-MAR Watershed Studies Study Design Report

California Department of Water Resources (DWR) | December 3rd, 2025

Click here to be taken to the California Department of Water Resources Watershed Studies home page

Click here to be taken to the California Department of Water Resources Watershed Studies home page

San Joaquin Basin Flood‑MAR Watershed Studies Basin-wide Summary and Next Steps

California Department of Water Resources (DWR) | December 3rd, 2025

The San Joaquin Basin Flood‑MAR Watershed Studies (Watershed Studies) — comprising five watershed reports for Calaveras, Stanislaus, Tuolumne, Merced and Upper San Jo

The San Joaquin Basin Flood‑MAR Watershed Studies (Watershed Studies) — comprising five watershed reports for Calaveras, Stanislaus, Tuolumne, Merced and Upper San Joaquin watersheds and a Basinwide Summary — deliver data-driven assessments of climate change vulnerabilities and adaptation that reveal risks and consequences and call for bold, coordinated solutions. In the San Joaquin Basin, the effects of climate change will exacerbate long-standing water management challenges. As these reports quantify, every water management sector — flood, water supply (surface and groundwater), and ecosystems — is vulnerable. Without bold action, the basin and its watersheds face mounting threats to communities, economies, and ecosystems. Although each watershed has unique characteristics, all confront a future climate that is hotter and characterized by more extreme weather. For flood management, the 2022 Central Valley Flood Protection Plan states clearly: Catastrophic flooding in the San Joaquin Basin is not a question of if, but when. Meanwhile, the reliability of water supplies is expected to worsen, and ecosystems face degradation.  Click here for the California Department of Water Resources Watershed Studies home page

San Joaquin Basin Flood‑MAR Watershed Studies Merced Watershed Study Area Report

California Department of Water Resources (DWR) | December 3rd, 2025

The San Joaquin Basin Flood‑MAR Watershed Studies (Watershed Studies) — comprising five watershed reports for Calaveras, Stanislaus, Tuolumne, Merced and Upper San Jo

The San Joaquin Basin Flood‑MAR Watershed Studies (Watershed Studies) — comprising five watershed reports for Calaveras, Stanislaus, Tuolumne, Merced and Upper San Joaquin watersheds and a Basin-wide Summary — deliver data‑driven assessments of climate change vulnerabilities and adaptation that reveal risks and consequences and call for bold, coordinated solutions. In the San Joaquin Basin, the effects of climate change will exacerbate long-standing water management challenges. As these reports quantify, every water management sector — flood, water supply (surface and groundwater), and ecosystems — is vulnerable. Without bold action, the basin and its watersheds face mounting threats to communities, economies, and ecosystems. Although each watershed has unique characteristics, all confront a future climate that is hotter and characterized by more extreme weather. For flood management, the 2022 Central Valley Flood Protection Plan states clearly: Catastrophic flooding in the San Joaquin Basin is not a question of if, but when. Meanwhile, the reliability of water supplies is expected to worsen, and ecosystems face degradation. Click here for the California Department of Water Resources Watershed Studies homepage