San Joaquin River

Habitat Restoration in the Sacramento-San Joaquin Delta and Suisun Marsh: A Review of Science Programs

Delta Stewardship Council (Delta Council) | April 25th, 2013

Current plans call for the restoration of tens of thousands of acres of mainly intertidal habitat in the Sacramento-San Joaquin Delta and Suisun Marsh. Restoration on thi

Current plans call for the restoration of tens of thousands of acres of mainly intertidal habitat in the Sacramento-San Joaquin Delta and Suisun Marsh. Restoration on this scale presents both formidable challenges and tremendous opportunities. As part of its legislatively mandated oversight of Delta science programs, the Delta Independent Science Board reviewed these habitat restoration efforts. We held discussions with individuals from state and federal agencies, NGOs, consulting firms, and universities. We were impressed by their dedication, enthusiasm, and knowledge, as well as by the scientific and institutional challenges they face. Our findings and observations about the restoration efforts are grouped under a series of criteria for a successful restoration program. In such a program: the goals are clearly articulated; the design incorporates spatial and temporal context, adaptive management and flexibility, and monitoring; modeling is used in design and evaluation; planning and implementation are coordinated among projects; the necessary scientific expertise is available; and stakeholders are involved early and often. Our findings and recommendations agree with those reached independently by National Research Council (NRC) panels. For convenience, as in the Delta Plan, we use "the Delta" to encompass both the statutory Delta and Suisun Marsh.

Harnessing the Power of Geophysical Imaging to Recharge California's Groundwater

American Geophysical Union (AGU) | April 17th, 2025

Motivated by the availability of 20,000 line-km of airborne electromagnetic (AEM) data covering the Central Valley of California, we developed a workflow that uses resist

Motivated by the availability of 20,000 line-km of airborne electromagnetic (AEM) data covering the Central Valley of California, we developed a workflow that uses resistivity profiles from electromagnetic (EM) data to assess the suitability of areas for groundwater recharge. We defined a suitable area as one where “fastpaths” of coarse-grained material could efficiently move water from the ground surface to the water table. We defined recharge metrics and generated the corresponding maps by integrating resistivity profiles from AEM data, sediment type (from driller's logs), water level measurements, and water quality measurements. The workflow is publicly available through a web-based application, fastpath. We produced maps displaying recharge metrics on a 400 m × 400 m grid covering the Central Valley, with 80% of the cells sufficiently close to an AEM resistivity profile (within ∼3 km) to be assessed for recharge. Various decisions are made in the workflow that result in a range of values for determined metrics at any given location. The maps summarizing all metrics show that between 19% (2,000,000 acres) and 56% (7,000,000 acres) of the total area in the valley is land suitable for recharge. The landcover with the largest total area of land classified as suitable is cultivated crops. We estimated the total space available for recharge water to be ∼170 km3 which is two orders of magnitude greater than an estimate of the total volume of water likely to be available for recharge.

HEC-HMS Models for the Sacramento and San Joaquin River Basins Comprehensive Study

U.S. Army Corps of Engineers (USACE) | August 1st, 2001

Due to several large and damaging flood events on the Sacramento and San Joaquin Rivers (California) during the 1980s and 1990s, the U.S. House of Representatives

Due to several large and damaging flood events on the Sacramento and San Joaquin Rivers (California) during the 1980s and 1990s, the U.S. House of Representatives directed the Sacramento District to develop comprehensive plans for flood control for the two rivers and to develop hydrologic and hydraulic models of the river systems. The models will be used to provide better forecasts and evaluations of flood damage reduction alternatives. Additionally, the model results will be used as input for reservoir simulation models. The Sacramento River Basin and the San Joaquin River/Tulare Lake Bed Basins comprise nearly 60,000 square miles, drain California’s Central Valley floor and receive much of their runoff from the Sierra Nevada mountain range. Developing hydrologic models for the tributary basins (which included extremely variable terrain) within a ten month time period was a formidable task. The District contacted the Hydrologic Engineering Center (HEC) to assist with the development of these models. HEC used the Hydrologic Modeling System program, HEC-HMS, and introduced the HEC-GeoHMS grid-based technology to perform the hydrologic study. GeoHMS is an ArcView® extension that provides automated subbasin delineation methods and calculates many physical characteristics used for estimation of hydrologic parameters. HEC developed and calibrated 33 individual HEC-HMS models for the major tributaries and portions of the valley floors of the Sacramento River Basin and the San Joaquin River / Tulare Lake Bed Basins. GeoHMS was used to delineate the individual river basins, perform initial subbasin delineation and develop the physical characteristics for the subbasins. Tools within GeoHMS allowed the modelers to iteratively redelineate their subbasins, as appropriate, to meet project needs. Keeping the modeling effort consistent was critical to the success of the study. To ensure this consistency of procedures and results, HEC developed modeling guidelines that each of the 11 modeling teams followed. Once the grid-based HEC-HMS models were developed, HEC contracted with the Corps’ Cold Regions Research and Engineering Laboratory (CRREL) to perform a snowmelt study for the watersheds. HEC provided a gridded precipitation file (4 km2) to CRREL. Through the use of their Distributed Snow Process Model (DSPM), CRREL then provided a gridded snowmelt/ precipitation file to HEC. DSPM computes snowmelt and rainfall depths at the soil surface on a grid-cell basis. This data is used directly by HEC-HMS as precipitation on the watershed. The ModClark rainfall to runoff transformation was used to compute the subbasin hydrographs. HEC-HMS parameter optimization models were developed at hourly flow gages for the unregulated headwater streams. The runoff parameter optimization models allowed the modelers to develop the runoff parameters necessary for the regression analysis. A number of physical characteristics were evaluated for correlation with variations in Clark’s time of concentration, TC, for the optimization models. The results of the regression analysis allowed the modelers to populate the ungaged subbasins with appropriate unit hydrograph parameters. Approximately 200 hourly flow gages and 83 reservoirs were considered in calibrating the models. The 33 individual basin models were then given to the Sacramento District.

Heresy in ENSO teleconnections: Atmospheric rivers as disruptors of canonical seasonal precipitation anomalies in the Southwestern US

Springer Nature | February 7th, 2025

In spite of forecasts for anomalous dryness based on the canonical La Niña signal, Water Years 2011, 2017, and 2023 brought copious precipitation to California and the S

In spite of forecasts for anomalous dryness based on the canonical La Niña signal, Water Years 2011, 2017, and 2023 brought copious precipitation to California and the Southwestern United States (SWUS). Although El Niño–Southern Oscillation (ENSO) is the main source of seasonal precipitation predictability for the region, outstanding Atmospheric River (AR) activity produced the unexpected regional wetness in each of these heretical water years (WYs). We define heretical WYs as those that result in precipitation anomalies that oppose those expected based on ENSO canon. We assess the contribution of ARs and other storms to these WYs, finding that heretical La Niña/El Niño WYs were characterized by anomalously robust/deficient AR activity. In California, precipitation accumulation during the heretical La Niña WYs was comparable to or even exceeded that observed during the exceedingly wet WY1998—the textbook canonical El Niño year. Our findings indicate a weaker/stronger relationship between ENSO and AR/non-AR precipitation, primarily driven by storm frequency. Although ARs can disrupt the ENSO-precipitation signal, ENSO still influences the frequency of AR precipitation in the southwestern U.S. desert, the region influenced by ARs that make landfall in Baja California, Mexico. These results highlight the complexity of ENSO's impact on precipitation in the Western US and underscore the need for a nuanced understanding of ENSO’s influence on ARs to improve seasonal precipitation prediction.

Hetch Hetchy Restoration Study

California Department of Water Resources (DWR) | July 17th, 2006

The restoration of Hetch Hetchy Valley on the upper Tuolumne River has once again captured the public’s imagination. In order to provide for an informed dialogue about

The restoration of Hetch Hetchy Valley on the upper Tuolumne River has once again captured the public’s imagination. In order to provide for an informed dialogue about this issue, the Resources Agency has objectively evaluated the many Hetch Hetchy Valley restoration studies produced during the past two decades. In so doing, the state also recognized the great value and benefit of providing a central clearinghouse of all Hetch Hetchy restoration work. Moreover, in conducting the study, the state provided a neutral, public forum to discuss issues related to Hetch Hetchy restoration, such as water supply and water quality, flood management, cultural resources, environmental impacts, energy generation, and recreation. In all, several hundred people participated in a July 2005 workshop in Sacramento and at other stakeholder meetings throughout the state. In addition, many interested Californians provided written comments for our consideration. This final report is a comprehensive analysis of Hetch Hetchy Valley restoration studies. But even as a comprehensive analysis, we find, first and foremost, that much study remains to be done because there are major gaps in vital information. For example, objectives for replacing the water supply for the Bay Area, dam removal methods and impacts, and considerations of the public use and benefit of a restored Valley remain largely undefined. Another critical, missing element is a formal public involvement process to engage agencies, Native American tribes, stakeholders and other interested parties in this issue. While we offer no formal recommendation about next steps, it is clear that further investigations into Hetch Hetchy Valley restoration cannot be led by the State of California alone. Federal participation will be important to help shape future studies and to work with the San Francisco Public Utilities Commission, tribes, and the public on any next steps in this process. Moving forward, the Resources Agency’s role in studies and planning for Hetch Hetchy will be consistent with the state’s approach to other significant natural resources such as the Sacramento-San Joaquin Delta or the Salton Sea — to protect the public trust by ensuring that these natural places are protected and utilized for the benefit of all Californians.

High Resolution Measurement of Levee Subsidence Related to Energy Infrastructure in the Sacramento-San Joaquin Delta

California Energy Commission (CEC) | August 31st, 2018

We assess flood overtopping potential (when flood water elevation exceeds levee elevation) to the levees surrounding the islands in the interior of California's S

We assess flood overtopping potential (when flood water elevation exceeds levee elevation) to the levees surrounding the islands in the interior of California's Sacramento-San Joaquin Delta. Because critical natural gas infrastructure is susceptible to overtopping-related disruption, we focus our analysis on regions that are crossed by the network of the state's natural gas pipelines. We use laser scanning data collected during 2015-2016 to estimate subsidence rates since 2007 when an earlier, Delta-wide, airborne laser-scanning topographic dataset was collected. For each levee studied, we combine: (1) the estimated subsidence rate, (2) a conservative range of sea-level rise projections and, (3) an estimate of the 100-year freshwater flood stage to project the time until exceedance of the federal levee height standard (PL84-99). We find that subsidence rates vary from 0-5 centimeters per year (cm/yr) with mean values of ~1-2 cm/year. Local gradients in subsidence can be on the order of cms/yr over a distance of 10s of meters parallel to the levee crests, and these types of gradients are present near some pipeline crossings. The Sherman Island region has subsidence rates close to a factor of 2 greater than other areas considered. Our projections indicate general ranges of exceedance date from about 2060 (fast sea-level rise scenario) to 2080 (slow sea-level rise scenario) with some places projected to exceed threshold by about 2050.

Highlights Central Valley Flood Protection Plan 2022 Update

California Department of Water Resources (DWR) | January 23rd, 2023

The 2022 Central Valley Flood Protection Plan Update was adopted by the Central Valley Flood Protection Board on December 16th, 2022. Just days later, beginning on Decemb

The 2022 Central Valley Flood Protection Plan Update was adopted by the Central Valley Flood Protection Board on December 16th, 2022. Just days later, beginning on December 27th, 2022, a series of atmospheric rivers began to impact California. This succession of atmospheric rivers resulted in 34 trillion gallons of water falling across California in 24 days, and 21 forecast points in the Central Valley reaching flood or monitor stage. Governor Gavin Newsom declared a state of emergency on January 4th, 2023; federal emergency and disaster declarations followed soon thereafter. These events underscore the importance of the CVFPP as the State’s strategic blueprint for investment in flood risk reduction in the Central Valley, especially in an era of whiplash weather—from drought to flooding— driven by the impacts of climate change.

History of Legislation and Policy Formation of the Central Valley Project

U.S. Department of Agriculture (USDA) | March 15th, 1946

History of the Delta Division, Central Valley Project

U.S. Bureau of Reclamation (USBR) | October 1st, 1994

The Delta Division of the Central Valley Project (CVP) acts as the hub around which the CVP revolves. The Delta Division contains the facilities that transfer water from

The Delta Division of the Central Valley Project (CVP) acts as the hub around which the CVP revolves. The Delta Division contains the facilities that transfer water from the Sacramento River, to bolster irrigation supplies to thirsty lands formerly dependent on water from the San Joaquin River. In time, the Delta Division became the hub for controversy revolving around the Central Valley Project. This document recounts the history of the Delta Division.  It was produced by the Bureau of Reclamation.

Holocene paleoclimate records from a large California estuarine system and its watershed region: linking watershed climate and bay conditions

Quaternary Science Reviews (Elsevier) | July 10th, 2006

The San Francisco Bay-Delta system includes a watershed that covers a large area of California and provides water to two-thirds of the State's population. Climate

The San Francisco Bay-Delta system includes a watershed that covers a large area of California and provides water to two-thirds of the State's population. Climate over the estuary and its watershed in the dry summer months is controlled by the subtropical high which dominates and deflects storms from California. The subtropical high weakens and migrates south as the Aleutian Low strengthens, bringing wet winter storms to the region. Paleoclimatic records from the Bay and its greater watershed, spanning the Holocene, are reviewed here in order to better understand natural variations of precipitation and runoff and the linkages between those variations and the salinity and ecosystems of the estuary. To better understand regional-scale climate patterns, paleoclimate records from coastal California and the Great Basin are also considered. Large fluctuations in climate have occurred during the period of interest, and there is generally good agreement between the paleoclimate records from different regions. Early Holocene climate throughout California was marked by rising temperatures and reduced moisture as seen in fire records from the watershed. This warmth and aridity peaked about 5000–7000 years ago and was followed by a cooling trend, with variable moisture conditions. The Estuary formed relatively rapidly in response to a high rate of sea level rise that dominated the Holocene until about 6000 years ago, and the subsequent reduced rate of inundation allowed vast tidal marshes to form along the edges of the estuary, which have since been recording changes in environmental conditions. The impacts of changing regional climate patterns are experienced in the San Francisco Bay-Delta system, as altered fresh water flows result in altered estuary salinity. For example, approximately 3800 cal yr B.P., records from throughout the state indicate a cool, moist period, and Bay salinity was reduced; this period was followed by a general drying trend throughout California over the last two millennia, punctuated by decades to centuries-long droughts and brief, extremely wet events. In particular, during the period ca. 1000–800 cal yr B.P. (A.D. 950–1150) conditions seem to have been unusually dry in many parts of the watershed, reducing the fresh water flows to the estuary, and shifting tidal marsh plant assemblages toward less diverse, but more salt-tolerant plants. In contrast, the Little Ice Age (ca. 550–200 cal yr B.P.) brought unusually cool and wet conditions to much of the watershed, and lowered salinity in the Bay. Many reconstructions suggest that notably stable conditions have prevailed over the instrumental period, i.e., after ca. A.D. 1850, even including the severe, short-term anomalies experienced during this period. Interdecadal variability is common in many of the records, with timescales of ca. 55, 70, 90, 100, 150, and 200 years.