San Joaquin River

2023 Water Resilience Portfolio Progress Report

California Natural Resources Agency (CNRA) | October 31st, 2023

2024 5-Year Review: Summary & Evaluation of Northern California Steelhead

National Oceanic and Atmospheric Administration (NOAA) | July 9th, 2024

Many West Coast salmon and steelhead (Oncorhynchus spp.) stocks have declined substantially from their historic numbers and now are at a fraction of their historical abun

Many West Coast salmon and steelhead (Oncorhynchus spp.) stocks have declined substantially from their historic numbers and now are at a fraction of their historical abundance. Several factors contribute to these declines, including: overfishing, loss of freshwater and estuarine habitat, hydropower development, poor ocean conditions, and hatchery practices. These factors collectively led to the National Marine Fisheries Service’s (NMFS) listing of 28 salmon and steelhead stocks in California, Idaho, Oregon, and Washington under the Federal Endangered Species Act (ESA). The ESA, under section 4(c)(2), directs the Secretary of Commerce to review the listing classification of threatened and endangered species at least once every 5 years. A 5-year review is a periodic analysis of a species’ status conducted to ensure that the listing classification of a species as threatened or endangered on the List of Endangered and Threatened Wildlife and Plants (List) (50 CFR 17.11 – 17.12; 50 CFR 223.102, 224.101) is accurate (USFWS and NMFS 2006; NMFS 2020). After completing this review, the Secretary must determine if any species should: (1) be removed from the list; (2) have its status changed from endangered to threatened; or (3) have its status changed from threatened to endangered. If, in the 5-year review, a change in classification is recommended, the recommended change will be further considered in a separate rule-making process. The most recent 5-year review analysis for West Coast salmon and steelhead occurred in 2016. This document describes the results of the 2024 review of ESA-listed Northern California steelhead (NC steelhead). A 5-year review is: • A summary and analysis of available information on a given species; • The tracking of a species’ progress toward recovery; • The recording of the deliberative process used to make a recommendation on whether or not to reclassify a species; • A recommendation on whether reclassification of the species is indicated.

21st century California drought risk linked to model fidelity of the El Niño teleconnection

Nature Portfolio (Springer Nature) | September 3rd, 2018

Greenhouse gas-induced climate change is expected to lead to negative hydrological impacts for southwestern North America, including California (CA). This includes a decr

Greenhouse gas-induced climate change is expected to lead to negative hydrological impacts for southwestern North America, including California (CA). This includes a decrease in the amount and frequency of precipitation, reductions in Sierra snow pack, and an increase in evapotranspiration, all of which imply a decline in surface water availability, and an increase in drought and stress on water resources. However, a recent study showed the importance of tropical Pacific sea surface temperature (SST) warming and an El Niño Southern Oscillation (ENSO)-like teleconnection in driving an increase in CA precipitation through the 21st century, particularly during winter (DJF). Here, we extend this prior work and show wetter (drier) CA conditions, based on several drought metrics, are associated with an El Niño (La Niña)-like SST pattern. Models that better simulate the observed ENSO-CA precipitation teleconnection also better simulate the ENSO-CA drought relationships, and yield negligible change in the risk of 21st century CA drought, primarily due to wetting during winter. Seasonally, however, CA drought risk is projected to increase during the non-winter months, particularly in the models that poorly simulate the observed teleconnection. Thus, future projections of CA drought are dependent on model fidelity of the El Niño teleconnection. As opposed to focusing on adapting to less water, models that better simulate the teleconnection imply adaptation measures focused on smoothing seasonal differences for affected agricultural, terrestrial, and aquatic systems, as well as effectively capturing enhanced winter runoff.

A Bayesian approach to infer nitrogen loading rates from crop and land-use types surrounding private wells in the Central Valley, California

European Geosciences Union (EGU) | May 7th, 2018

This study is focused on nitrogen loading from a wide variety of crop and land-use types in the Central Valley, California, USA, an intensively farmed region with high�

This study is focused on nitrogen loading from a wide variety of crop and land-use types in the Central Valley, California, USA, an intensively farmed region with high agricultural crop diversity. Nitrogen loading rates for several crop types have been measured based on field-scale experiments, and recent research has calculated nitrogen loading rates for crops throughout the Central Valley based on a mass balance approach. However, research is lacking to infer nitrogen loading rates for the broad diversity of crop and land use types directly from groundwater nitrate measurements. Relating groundwater nitrate measurements to specific crops must account for the uncertainty about and multiplicity in contributing crops (and other land uses) to individual well measurements, and for the variability of nitrogen loading within farms and from farm to farm for the same crop type. In this study, we developed a Bayesian regression model that allowed us to estimate land-use-specific groundwater nitrogen loading rate probability distributions for 15 crop and land-use groups based on a database of recent nitrate measurements from 2149 private wells in the Central Valley. The water and natural, rice, and alfalfa and pasture groups had the lowest median estimated nitrogen loading rates, each with a median estimate below 5 kg N ha -1 yr -1. Confined animal feeding operations (dairies) and citrus and subtropical crops had the greatest median estimated nitrogen loading rates at approximately 269 and 65 kg N ha -1 yr-1, respectively. In general, our probability-based estimates compare favorably with previous direct measurements and with mass-balance-based estimates of nitrogen loading. Nitrogen mass-balance-based estimates are larger than our groundwater nitrate derived estimates for manured and non-manured forage, nuts, cotton, tree fruit, and rice crops. These discrepancies are thought to be due to groundwater age mixing, dilution from infiltrating river water, or denitrification between the time when nitrogen leaves the root zone (point of reference for mass-balance derived loading) and the time and location of groundwater measurement.

A Comparative Study for Estimating Crop Evapotranspiration in the Sacramento-San Joaquin Delta

University of California, Davis (UC Davis) | April 23rd, 2018

Consumptive water use by crops, often referred to as evapotranspiration (ET), is frequently the largest component of an agricultural region’s water balance. This study

Consumptive water use by crops, often referred to as evapotranspiration (ET), is frequently the largest component of an agricultural region’s water balance. This study investigates crop consumptive use in the Sacramento-San Joaquin Delta (“Delta”) of California using a comparative approach with several prominent methods for estimating crop ET, including estimates based on crop coefficients, water balances, energy balance using remote sensing, and field measurements. Click here to download full report and links to appendices

A conceptual model for floodplains in the Sacramento-San Joaquin Delta

University of California, Davis (UC Davis) | October 3rd, 2012

Floodplains are among the most biologically productive and diverse ecosystems on Earth and they provide significant benefits to society such as attenuation of floodwaters

Floodplains are among the most biologically productive and diverse ecosystems on Earth and they provide significant benefits to society such as attenuation of floodwaters, groundwater recharge, filtration of nutrients and sediments, carbon sequestration, fisheries productivity and recreation.  However, floodplains are also among the most converted and threatened ecosystems.  Floodplain habitats in the Sacramento-San Joaquin Delta, and throughout California’s Central Valley, have been greatly reduced from their historic extent and key processes that create and maintain floodplains, such as flood flows and meander migration, have been greatly altered.  These widespread alterations to habitats and processes have lead to declines in many species’ populations in California’s Central Valley and Delta, creating challenges for both environmental and water management. To address these challenges numerous entities and programs are now focused on restoring floodplains and other Delta habitats.  This paper provides a conceptual model for floodplains that characterizes the key features and identifies the critical processes, drivers, and linkages that allow floodplains to produce a variety of functional outputs of management importance.  These outputs include: (1) the floodplain habitat mosaic, including riparian vegetation and its associated wildlife; (2) spawning and rearing habitat for native fish; and (3) food-web productivity that can support native fish on the floodplain as well as be exported to downstream ecosystems.  The model emphasizes that the production of these outputs from floodplains requires vertical and lateral hydrological connectivity across a broad range of flow conditions.  For example, long-duration flooding in the spring promotes native fish spawning and food-web productivity that benefits native species.

A Conjunctive Use Model for the Tule Groundwater Sub-Basin Area in the Southern-Eastern San Joaquin Valley, California

U.S. Bureau of Reclamation (USBR) | February 4th, 2003

The Tule groundwater sub-basin is an agriculturally-intensive area located in the eastern-central part of the southern San Joaquin Valley, California. Urban and a

The Tule groundwater sub-basin is an agriculturally-intensive area located in the eastern-central part of the southern San Joaquin Valley, California. Urban and agricultural stakeholders in the Tule sub-basin depend on a combination of imported surface water and pumped groundwater to meet their water demands. The water service districts there receive surface water deliveries from the Friant Unit of the Central Valley Project (CVP) (United States Bureau of Reclamation), the State Water Project (SWP) (California Department of Water Resources), the Kings River (United States Army Corps of Engineers), or the Success Reservoir (United States Army Corps of Engineers). All of these surface water sources develop their supplies from run-off and snow melt in the foothills and watersheds of the Sierra Nevada mountain range. The state of California is prone to recurring droughts, some lasting several years. During drought periods, irrigated agriculture depends more heavily on groundwater pumping as surface water supplies are generally less available. To buffer the effects of drought, districts in the Tule sub-basin have cooperatively managed their surface water and groundwater resources conjunctively. During a normal to wet year, excess available surface water supplies (e.g. releases for flood control) are used by some districts to recharge their groundwater reservoirs. However, a prolonged multi-year drought invariably leads to an increased dependence on groundwater pumping and overdraft of the groundwater sub-basin storage. In addition to climate variability, changes in future surface water supplies may also occur due to the passage of the Central Valley Project Improvement Act of 1992, which mandates that 400,000 acre-feet per year of CVP water be released from the Friant Unit into the San Joaquin River for restoration purposes. To better understand the impacts of irrigated agriculture, fluctuating surface water supplies, and groundwater pumping practices on water levels and groundwater storage in the Tule sub-basin area, we developed a GIS-based con- junctive use model to study them. The study area is 541,580 acres in size and contains the entire Tule groundwater sub-basin and parts of the Kaweah and Tulare Lake groundwater sub-basins. The incorporated land in the study area is divided into 26 water service districts: 21 irrigation, water, or public utility districts; 2 major cities; 2 private contractors; and 1 water company. These districts are either completely or partially located within the study area. The study area is further delineated into 9,114 individual land units from a 1985 land use survey of Tulare County. Agriculture is the largest land use, compris- ing 72% of the study area. Native and urban land use comprise 22% and 4% of the study area, respectively. Semi-agricultural and special conditions (i.e. fallow) land use each comprise 1%. Twelve crops account for 95% of the area under agricultural production. Cotton, grain & grass hay, citrus, vineyards, and alfalfa individually represent 20.3, 18.6, 13.6, 13, and 10.3% of the total productive acreage, respectively. Surface water supplies are distributed to the districts and ultimately to the individual land units by a surface water supply system. The surface water supply system in the model is divided into two parts: 1) an inter-district surface water channel network, and 2) an intra-district surface water distribution system. The inter-district channel network consists of the explicitly modeled source and diversion channels which import surface water into the study area and deliver it to individual districts. The intra-district distribution system con- sists of the implicitly modeled district channels (e.g. laterals, ditches, canals, farm turnouts) which deliver surface water to individual land units within each district. The conjunctive use model consists of three loosely-coupled sub-models: 1) a surface water supply (SWS) model, 2) an unsaturated zone water budget (UZWB) model, and 3) a groundwater flow model. The base period of the study covers the fiscal water years of 1970-99. The purpose of the SWS model is to calculate the surface water balance for the source and diversion channels in the inter-district channel network. For each modeled surface water channel, the SWS model computes surface water deliveries from it to each district and conveyance losses from it due to evaporation and channel seepage. The primary model outputs are monthly surface water deliveries to each district and monthly seepage rates from modeled channels. The surface water deliveries became input for the UZWB model. The channel seepage became input for the groundwater flow model as localized aquifer recharge. The allocation of surface water within each district, via the implicitly modeled intra-district surface water distribution system, is estimated by the UZWB model. The total imported surface water for 1970-99 from the CVP and the Success Reservoir are 13,329,262 and 4,653,501 acre-feet (af), respectively. The SWP and the Kings River imported the lesser amounts of 88,625 and 7,332 af, respec- tively. Annual CVP diversions varied from 125,970 af in 1977 to 679,298 af in 1993 with a 30-year annual average of 444,309 af. The Tule River and Pioneer Ditch both receive regulated releases from Success Reservoir. Tule River annual imports varied from 11,034 af in 1977 to 607,154 af in 1983 while the Pioneer Ditch varied from 3,445 af in 1973 to 5,874 af in 1990. The total natural runoff from the Deer Creek and White River from 1970-99 were 703,444 and 219,098 af, respectively. Deer Creek runoff varied from 4,082 af in 1992 to 103,716 af in 1983 while the White River runoff varied from 422 af in 1977 to 37,985 af in 1998. From 1970-99, a total of 15 million af of surface water was applied by the service districts in the study area. The applied surface water varied from a low of 135,482 af in 1977 to a high of 708,293 af in 1996. The Lower Tule River Ir- rigation District and the Delano-Earlimart Irrigation District together account for 59% of the total applied surface water while occupying approximately 40% of the incorporated area in the study area. Over the 30-year base period, an estimated total of 3.5 million af of seepage conveyance loss occurred in all sur- face water channels. Seepage in the Tule River, Deer Creek, and White River accounted for 85% of the total seepage. Total annual seepage varied from a low of 8,128 af in 1977 to 467,084 af in 1983. The UZWB model then calculates the monthly water storage changes in the soil root zone and deep vadose zone of each land unit, where the land unit is the UZWB model scale of resolution. It also models the intra-district surface water distribution system by estimating the monthly allocation of surface water to individual land units within each district. The main model outputs were the recharge to the unconfined aquifer from surface applied water and precipitation, and the groundwater pumping demand from the unconfined and confined aquifers. The recharge and groundwater pumping rates became input for the groundwater flow model. The total annual agricultural and urban consumptive use ranged from 865,800 af in 1970 to 1,246,700 af in 1999. The estimated total pumping ranged from 148,100 af in 1978 to 570,000 af in 1990. As expected, pumping was heaviest during the droughts of 1975-77 and 1987-92, and lightest during the wet years of 1973, 1978, 1982-83, 1995, and 1998. Precipitation totals varied from 177,800 af in 1990 to 974,400 af in 1998. Diffuse recharge from surface applied water ranged from 64,800 af in 1992 to 350,100 af in 1983. The net aquifer recharge for the entire study area was computed by ag- gregating the aquifer recharge and groundwater pumping of each land unit to this scale and adding the contribution to aquifer recharge from channel seepage. The monthly net recharge was then summed to produce a cumulative annual net recharge from 1970 to each fiscal water year from 1971-99. The water balance computed for the entire study area neglects horizontal groundwater inflows and outflows through its vertical boundaries. Groundwater fluxes undoubtedly exist along these boundaries. However, net fluxes are likely small in comparison to the total changes in storage due to vertical stresses applied to the entire study area (e.g. groundwater pumping, evapotranspiration, applied surface water, channel seepage). Horizontal groundwater flow on the inter-land unit and inter-district scales is expected to be more significant. For computing a total water balance, however, we made the simplifying assumption that the study area behaves as a relatively closed system where the net horizontal groundwater inflows through its vertical boundaries are small. Invoking this assumption, we then use the cumulative net recharge as an estimate of the cumulative groundwater storage change in the aquifer system. Ideally, verification of these estimates is performed by comparing them with an objective measure of the study area aquifer storage changes. However, changes in groundwater storage are not directly observable and must always be estimated using non-direct measures. As such, an objec- tive measure for verification does not exist. As an alternative, we compare the water balance model results with those produced by the water-table fluctuation (WTF) method. The trends in cumulative annual groundwater storage changes computed from the water balance and the WTF method from 1970-99 were quite similar. The minimum and maximum differences between them were 2,450 af (1980) and 752,387 af (1991), respectively. From 1970, the maximum amount of ground- water accumulation occurred in the spring of 1987 with the WTF method and the water balance estimating positive storage changes of 1,146,286 and 898,128 af, respectively. The maximum groundwater overdraft occurred in 1993 with the WTF method and the water balance estimating negative storage changes of 1,610,210 and 1,218,566 af, respectively. The 1987 and 1993 fiscal water years marked the beginning and ending of a major 6-year drought in California, respectively. Finally, the groundwater flow model calculates the changes in water levels in the aquifer system subject to transient groundwater recharge and pump- ing stresses. A post-processing routine calculates the cumulative groundwater storage changes over each district and the entire study area for each stress pe- riod. An automated calibration of the groundwater flow model was performed to refine the conceptual model of the hydrogeology and to estimate the spa- tial distributions of the aquifer system horizontal hydraulic conductivity. The calibration period of the groundwater flow model is 1970-85 and the validation period is 1986-99. Three different conceptual models of the aquifer system horizontal hydraulic conductivity, Kh, structure were evaluated in the calibration process: 1) Khas an exponential function of the specific yield, Sy, distribution, 2) Kh as a linear function of the saturated hydraulic conductivity of the soil survey map- ping units, and 3) division of the model domain into square zones of uniform size. The models were calibrated against both spatially distributed hydraulic head targets and cumulative groundwater storage change targets for seven of the largest districts. The discretization of the model domain into uniform square zones provided the most robust Kh structure and produced the most reason- able estimates of hydraulic head and district groundwater storage changes from the three conceptual models over the 1971-85 calibration period. The calibrated model was then used to compute the annual net inter-district groundwater fluxes between adjacent districts. In general, groundwater flux directions were con- sistent with the large-scale hydraulic gradients. Annual inter-district net fluxes between adjacent districts ranged from negligibly small ( < 100 af) to as much as 80,000 af (e.g. net flux from Lower Tule River ID to Pixley ID). Net inter-district fluxes were generally a function of the local transmissivity, the length of the shared border between adjacent districts, and the differences in their surface water supplies.

A Delta Renewed: A Guide to Science-Based Ecological Restoration in the Sacramento-San Joaquin Delta

San Francisco Estuary Institute (SFEI) | November 15th, 2016

This final report of the Delta Landscapes Project, A Delta Renewed, offers guidance for creating and maintaining landscapes that can provide desired ecological functi

This final report of the Delta Landscapes Project, A Delta Renewed, offers guidance for creating and maintaining landscapes that can provide desired ecological functions for decades to come. Based on extensive research into how the Sacramento-San Joaquin Delta used to function, how it has changed, and how it is likely to evolve, we make recommendations for how to re-establish the dynamic natural processes that can sustain native Delta wildlife as healthy populations into the future. The approach, building on work others have piloted and championed, is to restore or emulate natural processes where possible, establish an appropriate configuration of habitat types at the landscape scale, and use multi-benefit management strategies to create a more viable Delta ecosystem that can adapt and continue to provide valued functions as the climate changes. This approach is designed to integrate with the human landscape: ecosystem improvements as a part of a robust agricultural economy, water infrastructure and diversions, and urbanized areas. Strategic restoration which builds on the history and ecology of the region can contribute to the strong sense of place and recreational value of the Delta in the future. See more at: http://www.sfei.org/projects/delta-landscapes-project#sthash.RryQdaII.dpuf

A Delta Renewed: A Guide to Science-Based Ecological Restoration in the Sacramento-San Joaquin Delta

San Francisco Estuary Institute (SFEI) | November 1st, 2016

This report offers guidance for creating and maintaining landscapes in the Sacramento-San Joaquin Delta that support desired ecological functions, while retaining the ove

This report offers guidance for creating and maintaining landscapes in the Sacramento-San Joaquin Delta that support desired ecological functions, while retaining the overall agricultural character and water-supply service of the region. Based on extensive research into how the Delta functioned historically, how it has changed, and how it is likely to evolve, we discuss where and how to re-establish the dynamic natural processes that can sustain native Delta habitats and wildlife into the future. The approach, building on work others have piloted and championed, is to restore or emulate natural processes where possible, establish an appropriate mosaic of habitat types at the landscape scale, use multi-benefit management strategies to increase support for native species in agricultural and urban areas, and allow the Delta to adapt to future uncertainties of climate change, levee failure, and human population growth. With this approach, it will be critical to integrate ecological improvements with the human landscape: a robust agricultural economy, water infrastructure and diversions, and urbanized areas. Strategic restoration that builds on the history and ecology of the region can contribute to the strong sense of place and recreational value of the Delta.

A Delta Renewed: A Guide to Science-Based Ecological Restoration in the Sacramento-San Joaquin Delta

San Francisco Estuary Institute (SFEI) | November 1st, 2016

A Delta Renewed and the larger Delta Landscapes project are part of an ongoing effort to address these critically important challenges. They provide guidance for restora

A Delta Renewed and the larger Delta Landscapes project are part of an ongoing effort to address these critically important challenges. They provide guidance for restoration that renews critical functions over time without having major negative impacts on the current human enterprise in the Delta area and on other areas dependent on its services. The idea is to determine the most efficient ways to recover Delta functioning so that human benefits are maintained, while investing in process-based recovery of landscape functions. The scientists working on this project assume that this goal is best achieved if we can understand how the Delta functioned before major European modification. We can then use that knowledge as a guide to developing a diverse portfolio of habitats and connections that might sustain native species, and the attributes of a healthy Delta into the future. The effort to reconstruct the Delta of the early 1800s has been challenging, but is now completed. The next step is to devise management scenarios that will recover important functions and native species where possible. There is no intent to try to recreate the Delta of the past. That is impossible without sacrificing our objective of maintaining and even improving the human enterprises now present. What is essential now is to obtain general agreement among all of the stakeholders, which includes all citizens of California, that the Delta should be managed for the benefit of people and wildlife in a sustainable way. Given the uncertainties inherent in any large-scale reconciliation effort, there is a real need to appreciate the complex interactions and inter-dependencies that characterize the various components of the Delta landscape. There is also a need to understand the uncertainties of future climate change and to recognize the diversity of needs among our fellow citizens. Our hopes for success will ultimately depend on generating a spirit of cooperation for the common good. It won’t be easy, but the stakes are high. The Delta Landscapes project is dedicated to that goal.