Salton Sea Restoration Fund The State Has Not Fully Funded a Restoration Plan and the State’s Future Mitigation Costs Are Uncertain

California State Auditor | November 1st, 2013

The Salton Sea, located in Riverside and Imperial counties in Southern California, is the State’s largest inland lake. The Salton Sea was formed in 1905 when Colorado

The Salton Sea, located in Riverside and Imperial counties in Southern California, is the State’s largest inland lake. The Salton Sea was formed in 1905 when Colorado River floodwater breached an irrigation canal being constructed in the Imperial Valley; it has since been primarily fed by agricultural drain water. According to experts, the Salton Sea serves as an important fishery and wildlife habitat and is a major stopping point for migratory birds along the Pacific flyway. However, beginning in 2003, a series of agreements know collectively as the Quantification Settlement Agreement (QSA), between the State, local water agencies, and other entities have required, among other things, a water transfer that has reduced the amount of water that flows into the Salton Sea (water transfer). To mitigate the effects of the water transfer, the QSA requires one of the local water agencies that is a party to the agreement to provide additional water (mitigation water) to the Salton Sea for 15 years, from 2003 to 2017. Experts anticipate that when the Salton Sea stops receiving this mitigation water, the water transfer will cause profound negative environmental impacts, including the loss of fishery habitat, exposure of soils to wind erosion, and declines in bird species because of the loss of food.

Salton Sea Study Status Report

U.S. Bureau of Reclamation (USBR) | January 9th, 2003

The Salton Sea is located in a closed basin in Riverside and Imperial Counties in southern California, south of Indio and north of El Centro. The Sea is situated

The Salton Sea is located in a closed basin in Riverside and Imperial Counties in southern California, south of Indio and north of El Centro. The Sea is situated in a closed basin, more than 200 feet below sea level and has no natural outlet. Although lakes have existed in this basin in the past, the current body of water formed in 1905 when a levee break along the Colorado River caused flows from the Colorado River to enter the basin for about 18 months. Since 1905, the Sea has fluctuated in size with varying inflow, and it recently has had a surface area of 365 square miles. A balance between inflowing water and evaporation sustains the Sea. With no outlet, any salts that are dissolved in the inflow are trapped, although some do precipitate. Salt concentrations are currently about 44,000 milligrams per liter (mg/L), or about 25 percent higher than ocean water. Salinity will continue to rise under current conditions. It is highly likely that in the future, the inflow to the Sea will be less than it has been in the past. A reduction in inflow would cause the Sea to shrink and cause salinity to rise faster than it would have without a reduction in inflow. A gradual increase in salinity and its consequences was recognized soon after the Sea was formed. Formulation of salinity control measures was reported as early as the mid-1950s. Since then, many alternatives have been proposed and analyzed. The alternatives presented in this report were developed to address the goals contained in the Salton Sea Reclamation Act of 1998. The Act directs the Secretary of the Interior to study options for managing the salinity and elevation of the Sea in order to preserve fish and wildlife health and enhance opportunities for recreation use and economic development while continuing the Sea’s use as a reservoir for irrigation drainage. The Act required that certain options be analyzed and required consideration of reduced inflows down to 800,000 acre-feet or less per year. Consideration of any option that included importation of water from the Colorado River was prohibited. Reporting requirements of the Act were met on January 27, 2000, when Secretary Babbit forwarded a draft EIS/EIR and several other reports to Congress. Since then, analyses have continued on options presented in those reports and on new options. The development and transmission of this report is not required by law. This report provides a summary of the current status of the evaluation of alternatives currently under consideration. The primary purpose of the planning study was to evaluate possible methods of controlling the salinity and elevation of the Sea. The study also includes elements that address other issues at the Sea, such as high levels of nutrients. Fourteen alternatives providing a range of salinity and elevation control benefits and costs are presented in this report. For ease of presentation and understanding, alternatives were divided into the following categories: Salinity control alternatives Salinity and elevation control alternatives Causeway/barrier alternatives (the terms causeway and barrier are interchangeable in this report) Specialized diking alternatives Methods to control salinity and elevation include pumping water out of the Sea with discharge to some remote location; pumping water out of the Sea with discharge to local desalting plants or evaporation ponds, possibly in combination with enhanced evaporation systems that would require disposal of salt residues near or within the Sea; and dividing the Sea through the construction of dikes so that one portion serves to concentrate and isolate salts from the remainder of the Sea. Each alternative is discussed briefly below. The present value cost estimates for each alternative are also mentioned below. Present value cost includes the initial construction cost plus funds that would need to be set aside today to fund operation, maintenance, and energy over a 30-year period. This status report makes no recommendation regarding future action relating to restoration of the Salton Sea. In fact, given that all of the alternatives identified to date are extremely expensive, it is difficult, if not impossible, to make any recommendation without a decision by Congress regarding the relative importance of the Sea in light of other pressing national priorities.

San Joaquin River Restoration Program

San Joaquin River Restoration Program | December 13th, 2007

San Joaquin River Restoration Settlement

Congressional Research Service (CRS) | November 9th, 2007

Historically, Central California’s San Joaquin River supported large Chinook salmon populations. Since the Bureau of Reclamation’s Friant Dam on the San Joaquin River

Historically, Central California’s San Joaquin River supported large Chinook salmon populations. Since the Bureau of Reclamation’s Friant Dam on the San Joaquin River became fully operational in the 1940s, much of the river’s water has been diverted for off-stream agricultural uses. As a result, approximately 60 miles of the river bed is dry in most years. Thus, the river no longer supports Chinook salmon populations in its upper reaches. In 1988, a coalition of conservation and fishing groups sued Reclamation (Natural Resources Defense Council v. Rodgers). A U.S. District Court judge has ruled that operation of Friant Dam violates state law because of its destruction of downstream fisheries. Faced with mounting legal fees, uncertainty, and the possibility of dramatic cuts to water diversions, parties negotiated a settlement instead of proceeding to trial. In September 2006, an agreement, commonly called the Settlement, was reached. It calls for new releases of water from Friant Dam to restore fisheries, as well as for efforts to mitigate reductions in off-stream deliveries lost to restoration flows. Congressional authorization and appropriations are required for full Settlement implementation. Legislation based on the Settlement (H.R. 4074, H.R. 24 and S. 27) is pending. Related bills have also been introduced. A key legislative issue is how to finance the Settlement, specifically how to resolve congressional pay-as-you-go (PAYGO) issues. Other challenges are how to achieve the Settlement’s dual goals of fisheries restoration and water management, and how to address concerns of stakeholders not party to the Settlement, without disrupting the negotiated agreement. The amount of water projected for restoration flows and the volume of reduced Friant water deliveries are related, but the relationship would not necessarily be one-for-one. Available estimates for total annual Friant water supplies (including both contract and temporary water) are, on average, 15% to 16% less under the Settlement than under current operations; but such estimates do not account for improvements in water management that might reduce the impact on water users. For three-quarters of water contractors, the reduction would represent a reduction in one of their available sources of water. The impacts of such reductions will vary by contractor depending on the firmness of existing surface water supplies and the reliability of groundwater supplies. How to offset the decrease and who would pay for investments in other water sources and improved efficiency has not been determined. Although the region may benefit from increased recreational expenditures and investment in river restoration activities under the Settlement, studies suggest its largest and mostly negative economic impact would be on the agriculture industry, at least in the short term. In addition, downsteam interests not party to the Settlement have been concerned about increased flooding, groundwater infiltration, and competition with existing federal financial commitments. Nearby communities fear harm to groundwater quantity and quality. Some of these concerns have been addressed in the legislation, but some remain. On the other hand, some communities and interests believe restoration will bring other benefits to the river, such as improved surface water quality in lower San Joaquin River reaches. Ultimate Settlement costs and benefits are very difficult to predict.

Scott Valley Integrated Hydrologic Model: Data Collection, Analysis, and Water Budget Final Report

University of California, Davis (UC Davis) | November 14th, 2017

The Scott Valley is an agricultural groundwater basin in Northern California, within the Scott River watershed and part of the much larger Klamath Basin watershed straddl

The Scott Valley is an agricultural groundwater basin in Northern California, within the Scott River watershed and part of the much larger Klamath Basin watershed straddling the California-Oregon border. The Scott River provides important habitat for salmonid fish, including spawning and rearing habitat for coho and fall-run Chinook salmon and steelhead trout. Sufficient flows at adequately low temperatures during summer, for rearing, and fall, for spawning, are critical for healthy fish habitat in the mainstem and tributaries. This report presents the data assembled and the methods used for data analysis and data modeling to prepare the Scott Valley Integrated Hydrologic Model Version 2, which is currently under development. The report includes precipitation data analysis, streamflow data analysis and modeling, geology and groundwater data review and analysis, evapotranspiration and soils data analysis, and preparation of relevant watershed, land use, topography, and irrigation data. The data collection and analysis efforts culminate in the development of a spatio-temporally distributed soil water budget model for the Scott Valley. The soil water budget model is used to determine spatially and temporally varying groundwater pumping rates, surface water diversion rates, and groundwater recharge across the groundwater basin. The spatial resolution of the soil water budget model is by individual fields (land use polygons). Temporal discretization is in daily time steps for the period from October 1, 1990 to September 30, 2011. This period includes several dry years, average years, and wet year periods. Methods and results of the soil water budget model are presented in this report. This report represents the next step toward a better understanding of the interactions between groundwater, surface water, land-use, and agricultural practices with a specific focus on the seasonal impacts of groundwater pumping on streamflow during critical low flow periods. The work presented here relies on an extensive data collection facilitated by the voluntary and active collaboration of communities, landowners, the Scott River Watershed Council (SRWC), the Siskiyou Resource Conservation District (SRCD), and the Scott Valley Groundwater Advisory Committee (GWAC) which has been appointed by the Board of Supervisors in January 2011, meeting monthly since April 2011 and advising UC Davis on its data collection and modeling efforts. In the data analysis and during the model development, numerous assumptions have been made as is common in building a conceptual and numerical integrated hydrologic model. Models cannot represent the complexity of the real system, but are an effort to capture salient hydrologic features with sufficient accuracy to develop modeling results that are useful for a better understanding of the watershed dynamics and water balance.

Sediment Mobility and River Corridor Assessment for a 140-Kilometer Segment of the Main-Stem Klamath River Below Iron Gate Dam, California

U.S. Geological Survey (USGS) | January 26th, 2021

This river corridor assessment documents sediment mobility and river response to flood disturbance along a 140-kilometer segment of the main-stem Klamath River below Iron

This river corridor assessment documents sediment mobility and river response to flood disturbance along a 140-kilometer segment of the main-stem Klamath River below Iron Gate Dam, California. Field and remote sensing methods were used to assess fundamental indicators of active sediment transport and river response to a combination of natural runoff events and reservoir releases during the study period from 2005 to 2019. Discharge measurements at two gaged sites and bed-material samples at two ungaged sites provided direct and indirect evidence of mobile bed conditions, scour and fill, and surface flushing of fine sediment. Available remote-sensing datasets collected in 2005, 2009, 2010, and 2016 were used to determine sediment storage, flood inundation boundaries, and provide indirect evidence of flood-induced scour. These datasets validate channel-maintenance flows defined by Shea and others (2016). During the study period, flows greater than or equal to 6,030 cubic feet per second mobilized the substrate, caused localized scour, and flushed fine sediment from bar surfaces. Flows greater than or equal to 10,400 cubic feet per second stripped vegetation from bars and floodplains and produced deeper scour. Flood disturbance within the study reach is produced by the combined effect of natural flows and reservoir releases, which resulted in mobile bed conditions during the study period. Periodic scour and substrate disturbance are considered by the U.S. Fish and Wildlife Service to be integral for managing disease-induced mortality of juvenile and adult salmonids. Substrate conditions conducive to parasites that host infectious diseases, particularly Ceratonova shasta, occur periodically. Additional studies are required to determine whether disease prevalence can be mitigated by well-timed reservoir releases. Study results are useful for interpreting linkages among physical and biological processes and for evaluating the effectiveness of flow management targeted to improve river bed conditions for endangered salmonid populations.

Sediment Transport in Two Tributaries to the San Joaquin River Immediately Below Friant Dam—Cottonwood Creek and Little Dry Creek, California

U.S. Geological Survey (USGS) | May 2nd, 2023

Two tributaries to the greater San Joaquin River watershed, Cottonwood and Little Dry Creeks, in California’s Central Valley, were assessed for sediment and streamflow

Two tributaries to the greater San Joaquin River watershed, Cottonwood and Little Dry Creeks, in California’s Central Valley, were assessed for sediment and streamflow dynamics between October 1, 2011, and September 30, 2019. The two systems deliver sediment to the San Joaquin River below Friant Dam, California. Dams create downstream discontinuities in streamflow and sediment transport and therefore influence fish habitat and sediment dynamics. Because these two creeks are directly downriver from Friant Dam, they become the most upstream source of sediment to the San Joaquin River below Friant Dam. The quality and quantity of spawning habitat for fish in the gravel-bedded reach of the San Joaquin River relies on a range of bed material particle size suitable for redd structure. The effects of coarse-sand to fine-gravel supply on salmonid habitat depends primarily on the size of the sediment and the timing of its addition from tributaries to the San Joaquin River; thus, understanding the timing, quantity, and size of sediment supplied from these two tributaries is critical to the management of ecological and biological sustainability. Streamflow from Cottonwood and Little Dry Creeks, along with streamflow from the San Joaquin River below Friant Dam, were compared to continuously measured water-surface elevations to quantify the timing and direction of streamflow. Suspended-sediment samples were collected with multiple automatic samplers and analyzed for concentration and grain-size distribution. Measured suspended-sediment concentrations and streamflows were used to develop sediment rating curves and compute continuous estimates of suspended-sediment load for each tributary. Satellite imagery was used to qualify spatial and temporal dynamics through the lower watersheds and support more quantitative sediment-load estimates. Computed annual sediment loads ranged from 1.32x101 to 2.68x104 metric tons for Little Dry Creek and 9.82 to 1.98x103 metric tons for Cottonwood Creek. Sediment loads computed during the study period for both watersheds show that annual loads were highest during water year 2017 (October 1, 2016, to September 30, 2017). Sediment transport primarily occurred between the months of January and March. In both tributaries, grain-size distributions of suspended sediment were predominantly coarse-sized sand and were finer than the remnant bed material. Both creeks demonstrate backwater effects from the San Joaquin River, but the more tortuous stream channel and historical mining pits within Little Dry Creek provide more capacity for sediment storage compared to the less complex stream network of Cottonwood Creek. Because loads were computed based on upstream streamgages and not at the confluence of each tributary to the San Joaquin River, annual load estimates do not represent direct flux into the San Joaquin River; instead, these results indicated that in Little Dry Creek, particularly, the lowest portion of the watershed stores sediment before it reaches the San Joaquin River.

Selenium in Muscle Plugs of White Sturgeon from North San Francisco Bay, 2015-2017

San Francisco Estuary Institute (SFEI) | February 1st, 2019

This report presents the findings from a study evaluating selenium concentrations in white sturgeon (Acipenser transmontanus) muscle tissues collected from live sturgeon

This report presents the findings from a study evaluating selenium concentrations in white sturgeon (Acipenser transmontanus) muscle tissues collected from live sturgeon during the California Department of Fish and Wildlife’s fall sturgeon tagging studies in North San Francisco Bay. The goal of this study was to non-lethally collect a large number of sturgeon muscle plugs and analyze them for selenium to (1) establish an understanding of current status, trends, and causes of variability in sturgeon muscle selenium concentrations; and (2) evaluate the potential for long-term sturgeon selenium monitoring with muscle plugs, through development of field and laboratory methods and informing the monitoring design. Monitoring of selenium in white sturgeon is needed to evaluate the effectiveness of the North Bay Selenium Total Maximum Daily Load (TMDL) in protecting sturgeon from selenium toxicity. This technical report provides documentation of the study and presents its major findings in the context of all historically available data on sturgeon muscle selenium concentrations in San Francisco Bay. 

Selenium in White Sturgeon Tissues: 2015 Sturgeon Derby

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

The Original Sturgeon Derby (Derby) is an annual fishing derby held in Bay Point, CA that presents an opportunity to collect and analyze a variety of tissue samples from

The Original Sturgeon Derby (Derby) is an annual fishing derby held in Bay Point, CA that presents an opportunity to collect and analyze a variety of tissue samples from angler-harvested white sturgeon (Acipenser transmontanus) for selenium (Se). Collection and analysis of these tissues from the 2015 Derby helped to: 1) develop non-lethal sampling methods and 2) better understand the correlation between tissues that can be collected non-lethally (muscle plug, fin ray) with those that are of greater toxicological interest (ovary, liver). Otolith samples were also collected to inform the development of methods for fin ray Se microchemical analysis. On January 31 and February 1, 2015, tissue samples were obtained from eight female and 19 male white sturgeon collected at the Derby and analyzed for Se. The fin rays were also used to estimate age of the fish, and the muscle plugs were analyzed for carbon (δ13 C), nitrogen (δ15 N), and sulfur (δ34 S) isotope ratios to provide information about recent habitat (e.g., primarily Delta, North Bay, or ocean) and foraging behavior (e.g., primarily clam- or fish-based diet). 

Shasta Dam Fish Passage Evaluation – Pilot Implementation Plan – U.S. Bureau of Reclamation

U.S. Bureau of Reclamation (USBR) | September 1st, 2015