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Ground Water in the Central Valley, California - A Summary Report

U.S. Geological Survey (USGS) | June 1st, 1991

Summary

The agricultural productivity of the Central Valley depends on irrigation. Half of the 22 million acre-feet of irrigation water applied annually is ground water. The va

The agricultural productivity of the Central Valley depends on irrigation. Half of the 22 million acre-feet of irrigation water applied annually is ground water. The valley is a long, narrow structural trough filled with about 32,000 feet of sediment in the south and as much as 50,000 feet in the north. Nearly all the fresh ground water is contained in the continental rocks and deposits younger than Eocene age. Streamflow, an important factor in recharging the aquifer system, is influenced by precipitation in the mountains surrounding the valley. The majority of recharge from infiltration of streamflow occurs on the east side of the valley. Ground-water pumpage, which greatly exceeds the natural recharge rate, has dramatically altered the ground-water flow in the Central Valley. During the 1960's and 1970's, the recharge rate was more than five times that of the predevelopment period and was largely derived from percolation of imported surface water or recirculated pumped ground water rather than precipitation and recharge from streams. Prior to development, most ground water was discharged as evapotranspiration; however, in recent years, most discharge has been well pumpage. Computer simulation of the Central Valley aquifer system suggests that the total flow through the system has increased from about 2 million acre-feet per year to nearly 12 million acre-feet per year. The vertical movement of ground water has been artificially enhanced by many of the 100,000 irrigation wells that contain long intervals of perforated casing. When unpumped, these wells permit vertical flow between permeable layers within the aquifer system. The total fresh ground water presently (1986) in storage in the upper 1,000 feet of the aquifer system is about 800 million acre-feet. During the 1960's and 1970's, ground water in storage was depleted at an average rate of 800,000 acre-feet annually. In the San Joaquin Valley from the 1940's to the late 1960's, substantial withdrawals of ground water were accompanied by hundreds of feet of head decline. This head decline caused inelastic compaction of fine-grained beds, resulting in land subsidence that is unequaled anywhere else in the world. More than one-half of the San Joaquin Valley (or about 5,200 square miles) underwent subsidence of more than 1 foot. In one location, subsidence exceeded 29 feet. Within the areas of heavy withdrawals, subsidence is greatest where the aquifer system contains thick sections of montmorillonite clay. Land subsidence created engineering and economic problems, including damage to canals and drainage systems, and loss of irrigation wells caused by casing failure. More recently (since the drought of 1976-77), surface-water imports have increased, ground-water pumpage has decreased, and in places, ground-water levels have recovered. Land subsidence has virtually ceased; however, it could resume with increased pumpage, if water levels decline below previous lows. Ground-water quality in the Central Valley is generally influenced by the water from streams that are a major source of recharge. In general, water on the east side of the valley and from east-side streams contains low concentrations of dissolved solids compared to water on the west side and from west-side streams. Concentrations of dissolved solids in ground water generally are lower in the northern part of the valley than in the southern part. There are, however, localized exceptions in many places through the valley. Local concentrations of boron, chloride, and nitrate in the ground water of the Central Valley are large enough to be a problem either to crops or humans. Human activities have some influence on the concentration and location of water-quality problems in the valley. Significant increases in concentrations of dissolved solids and, specifically, dissolved nitrate indicate that ground-water quality is degrading as a result of increasing application of fertilizer in agricultural areas and the growth of urban population. Pesticides such as dibromochloropropane (DBCP) as well as selenium and other trace elements in agricultural drainage water cause ecological and health problems in the San Joaquin Valley.

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Groundwater Contributions of Flow, Nitrate, and Dissolved Organic Carbon to the Lower San Joaquin River, California, 2006–08

U.S. Geological Survey (USGS) | October 8th, 2013

Summary

The influence of groundwater on surface-water quality in the San Joaquin River, California, was examined for a 59-mile reach from the confluence with Salt Slough to Verna

The influence of groundwater on surface-water quality in the San Joaquin River, California, was examined for a 59-mile reach from the confluence with Salt Slough to Vernalis. The primary objective of this study was to quantify the rate of groundwater discharged to the lower San Joaquin River and the contribution of nitrate and dissolved organic carbon concentrations to the river. Multiple lines of evidence from four independent approaches were used to characterize groundwater contributions of nitrogen and dissolved organic carbon. Monitoring wells (in-stream and bank wells), streambed synoptic surveys (stream water and shallow groundwater), longitudinal profile surveys by boat (continuous water-quality parameters in the stream), and modeling (MODFLOW and VS2DH) provided a combination of temporal, spatial, quantitative, and qualitative evidence of groundwater contributions to the river and the associated quality. Monitoring wells in nested clusters in the streambed (in-stream wells) and on both banks (bank wells) along the river were monitored monthly from September 2006 to January 2009. Nitrate concentrations in the bank wells ranged from less than detection—that is, less than 0.01 milligrams per liter (mg/L) as nitrogen (N)—to approximately 13 mg/L as N. Nitrate was not detected at 17 of 26 monitoring wells during the study period. Dissolved organic carbon concentrations among monitoring wells were highly variable, but they generally ranged from 1 to 4 mg/L. In a previous study, 14 bank wells were sampled once in 1988 following their original installation. With few exceptions, specific conductivity and nitrate concentrations measured in this study were virtually identical to those measured 20 years ago. Streambed synoptic measurements were made by using a temporarily installed drive-point piezometer at 113 distinct transects across the stream during 4 sampling events. Nitrate concentrations exceeded the detection limit of 0.01 mg/L as N in 5 percent of groundwater samples collected from the in-stream wells as part of the synoptic surveys. Only 7 of the 113 cross-sectional transects had nitrate concentrations greater than 1 mg/L as N. In contrast, surface waters in the San Joaquin River tended to have nitrate concentrations in the 1–3 mg/L as N range. A zone of lower oxygen (less than 2 mg/L) in the streambed could limit nitrate contributions from regional groundwater flow because nitrate can be converted to nitrogen gas within this zone. Appreciable concentrations of ammonium (average concentration was 1.92 mg/L as N, and 95th percentile was 10.34 mg/L as N) in the shallow groundwater, believed to originate from anoxic mineralization of streambed sediments, could contribute nitrogen to the overlying stream as nitrate following in-stream nitrification, however. Dissolved organic carbon concentrations were highly variable in the shallow groundwater below the river (1 to 6 ft below streambed) and generally ranged between 1 and 5 mg/L, but had maximum concentrations in the 15–25 mg/L range. The longitudinal profile surveys were not particularly useful in identifying groundwater discharge areas. However, the longitudinal approach described in this report was useful as a baseline survey of measured water-quality parameters and for identifying tributary inflows that affect surface-water concentrations of nitrate. Results of the calibrated MODFLOW model indicated that the simulated groundwater discharge rate was approximately 1.0 cubic foot per second per mile (cfs/mi), and the predominant horizontal groundwater flow direction between the deep bank wells was westward beneath the river. The modeled (VS2DH) flux values (river gain versus river loss) were calculated for the irrigation and non-irrigation season, and these fluxes were an order of magnitude less than those from MODFLOW. During the irrigation season, the average river gain was 0.11 cfs/mi, and the average river loss was ?0.05 cfs/mi. During the non-irrigation season, the average river gain was 0.10 cfs/mi, and the average river loss was 0.08 cfs/mi.

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Groundwater Quality in the Sacramento Metropolitan Shallow Aquifer, California

U.S. Geological Survey (USGS) | May 2nd, 2019

Summary

The Sacramento metropolitan (SacMetro) study unit covers approximately 3,250 square kilometers of the Central Valley along the eastern edge of the northern and southern e

The Sacramento metropolitan (SacMetro) study unit covers approximately 3,250 square kilometers of the Central Valley along the eastern edge of the northern and southern ends of the San Joaquin and Sacramento Valleys, respectively. Groundwater withdrawals supply a significant portion of the water-resource needs of the region. In the southern portion of the study unit, groundwater accounts for nearly 90 percent of water demand in the area (South Area Water Council, 2011). Groundwater sampled in the SacMetro study unit comes from alluvial aquifers primarily composed of sediments derived from the Sierra Nevada Mountains to the east. Recharge to the groundwater system is primarily from the streams draining the Sierra Nevada, and from precipitation and infiltration of applied irrigation water (California Department of Water Resources, 2003). The public-supply aquifer system assessments of this area in 2005 found elevated concentrations of inorganic constituents including arsenic, iron, and manganese as well as of solvents in some wells (Bennett and others, 2010; 2011). This study was designed to provide a statistically representative assessment of the quality of groundwater resources used for domestic drinking water in the SacMetro study unit. A complete listing of what was measured, including the sampling results, are presented in Bennett and others, 2019. A total of 49 wells were sampled between July 2017 and November 2017 (Bennett and others, 2019). The wells in the study were 32–160 meters deep, and water levels were 1–62 meters below land surface.

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Groundwater Quality in the South Coast Interior Basins, California

U.S. Geological Survey (USGS) | May 14th, 2014

Summary

The South Coast Interior Basins (SCI) study unit covers approximately 653 square miles and consists of the Livermore, Gilroy-Hollister, Cuyama Valley, Castac Lake Valley,

The South Coast Interior Basins (SCI) study unit covers approximately 653 square miles and consists of the Livermore, Gilroy-Hollister, Cuyama Valley, Castac Lake Valley, Cuddy Canyon Valley, Cuddy Ranch Area, Cuddy Valley, and Mil Potrero groundwater basins (California Department of Water Resources, 2003). These basins were grouped into three study areas based on geography: Livermore (LIV), Gilroy (GIL), and Cuyama (CUY) (Mathany and others, 2009). Average annual precipitation across the study unit varies among the three study areas—from more than 20 inches (in.) along the northwest margin of the LIV study area to less than 8 in. in the northern parts of the CUY study area. The study areas are drained by the Arroyo de la Laguna canal in LIV, the Pájaro River and the San Benito River in GIL, and the Cuyama River in CUY. The primary aquifer system consists of Plio-Pleistocene sedimentary formations, Tertiary to Holocene-age alluvial sedimentary sequences, and unconfined Holocene- age and Pleistoceneage alluvium. The primary aquifer system is defined as those parts of the aquifers corresponding to the perforated intervals of the public-supply wells listed in the California Department of Public Health (CDPH) database. Public-supply wells in the study unit are typically drilled to depths between 200 and 600 feet, consist of solid casing from the land surface to a depth of about 50 to 350 feet, and are perforated below the solid casing. Water quality in the primary aquifer system may differ from that in the shallower and deeper parts of the aquifer system. Land use within 500-meter buffer areas around the wells in the study unit is approximately 44 percent (%) agricultural, 29% urban, and 27% natural. Agricultural lands are mostly orchards, row crops, vineyards, or pastures. The largest urban areas are the cities of Livermore and Gilroy. Recharge to groundwater basins occurs as infiltration of spring and streamflow, direct infiltration of precipitation and irrigation, subsurface inflow, and engineered recharge (percolation ponds and river regulation). The primary sources of groundwater discharge are water pumped for irrigation and municipal supply, discharge to rivers and streams, and evaporation.

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Groundwater Quality in the Western San Joaquin Valley, California

U.S. Geological Survey (USGS) | June 9th, 2017

Summary

Groundwater provides more than 40 percent of California’s drinking water. To protect this vital resource, the State of California created the Groundwater Ambient Monito

Groundwater provides more than 40 percent of California’s drinking water. To protect this vital resource, the State of California created the Groundwater Ambient Monitoring and Assessment (GAMA) Program. The Priority Basin Project of the GAMA Program provides a comprehensive assessment of the State’s groundwater quality and increases public access to groundwater-quality information. The Western San Joaquin Valley is one of the study units being evaluated.

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Human Costs of Nitrate-contaminated Drinking Water in the San Joaquin Valley

Pacific Institute | March 1st, 2011

Summary

While most Californians take for granted that safe water is readily available at the turn of a tap, a growing number of communities, primarily in the San Joaquin Valley a

While most Californians take for granted that safe water is readily available at the turn of a tap, a growing number of communities, primarily in the San Joaquin Valley and other agricultural areas of the state, face very real impacts from nitrate contamination of the drinking water sources serving their homes and schools. New research led by the Pacific Institute, The Human Costs of Nitrate-Contaminated Drinking Water in the San Joaquin Valley, finds that nitrate contamination of groundwater has wide-reaching effects on California’s health, economic vitality, and environmental well being, disproportionately affecting low-income households and Spanish-speaking residents. The analysis brings a stark reality check to the fore as the Central Valley Water Board considers a new regulatory program for irrigated lands, the primary source of nitrate contamination in the San Joaquin Valley. There have never been any regulatory requirements on irrigated agriculture to protect groundwater from fertilizers, which are the primary source of nitrate in the valley. Nitrate levels have increased dramatically in drinking water supplies over the last few decades. The new study, The Human Costs of Nitrate-Contaminated Drinking Water in the San Joaquin Valley, a collaboration of the Pacific Institute, Community Water Center, Clean Water Fund, and California Rural Legal Assistance Foundation, focuses on the household costs of avoiding nitrate-contaminated drinking water connected to community water systems and the costs to these systems of removing or avoiding nitrates, and it points to key policies and further research needed to better understand and resolve this entrenched challenge. The eight-county San Joaquin Valley has some of the most contaminated aquifers in the nation: 92 drinking water systems in the San Joaquin Valley had a well with nitrate levels above the legal limit from 2005-2008, potentially affecting the water quality of approximately 1.3 million residents. In addition to public water systems, the State Water Board sampled 181 domestic wells in Tulare County in 2006 and found that 40% of those tested had nitrate levels above the legal limit.

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Impacts of the 2014 severe drought on the Microcystis bloom in San Francisco Estuary

Harmful Algae (Elsevier) | February 17th, 2017

Summary

The increased frequency and intensity of drought with climate change may cause an increase in the magnitude and toxicity of freshwater cyanobacteria harmful algal blooms

The increased frequency and intensity of drought with climate change may cause an increase in the magnitude and toxicity of freshwater cyanobacteria harmful algal blooms (CHABs), including Microcystis blooms, in San Francisco Estuary, California. As the fourth driest year on record in San Francisco Estuary, the 2014 drought provided an opportunity to directly test the impact of severe drought on cyanobacteria blooms in SFE. A field sampling program was conducted between July and December 2014 to sample a suite of physical, chemical, and biological variables at 10 stations in the freshwater and brackish reaches of the estuary. The 2014 Microcystis bloom had the highest biomass and toxin concentration, earliest initiation, and the longest duration, since the blooms began in 1999. Median chlorophyll a concentration increased by 9 and 12 times over previous dry and wet years, respectively. Total microcystin concentration also exceeded that in previous dry and wet years by a factor of 11 and 65, respectively. Cell abundance determined by quantitative PCR indicated the bloom contained multiple potentially toxic cyanobacteria species, toxic Microcystis and relatively high total cyanobacteria abundance. The bloom was associated with extreme nutrient concentrations, including a 20-year high in soluble reactive phosphorus concentration and low to below detection levels of ammonium. Stable isotope analysis suggested the bloom varied with both inorganic and organic nutrient concentration, and used ammonium as the primary nitrogen source. Water temperature was a primary controlling factor for the bloom and was positively correlated with the increase in both total and toxic Microcystis abundance. In addition, the early initiation and persistence of warm water temperature coincided with the increased intensity and duration of the Microcystis bloom from the usual 3 to 4 months to 8 months. Long residence time was also a primary factor controlling the magnitude and persistence of the bloom, and was created by a 66% to 85% reduction in both the water inflow and diversion of water for agriculture during the summer. We concluded that severe drought conditions can lead to a significant increase in the abundance of Microcystis and other cyanobacteria, as well as their associated toxins.

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Land use and land cover influence on water quality in the last free-flowing river draining the western Sierra Nevada, California

Journal of Hydrology (Elsevier) | November 10th, 2005

Summary

Land use and land cover across 28 sub-basins within the Cosumnes Watershed, CA (1989 km2) were correlated to nitrate-N and total suspended solids (TSS) loading between w

Land use and land cover across 28 sub-basins within the Cosumnes Watershed, CA (1989 km2) were correlated to nitrate-N and total suspended solids (TSS) loading between water years 1999 and 2001. The impact of human development on stream water quality was evident as both agricultural area and population density predicted TSS loading in a linear mixed effects model. In contrast to the TSS model, the nitrate-N loading model was more complex with agriculture, grassland, and the presence or absence of waste water treatment plants (WWTPs) all contributing. The lack of correlation between population density and nitrate-N loading indicates that human habitation of the landscape does not impact stream nitrate levels until a WWTP is built within the sub-basin. During dry water years the models predict a linear reduction in TSS loading but the correlations to agriculture and population density remain positive. In contrast, nitrate is positively correlated to grasslands during average water years and negatively correlated during dry water years. Analysis of constituent fluxes from the upper watershed versus the lower watershed indicates that silica is derived primarily from the uplands and that during dry water years the upper watershed is an important source of dissolved organic carbon (DOC) and nitrate. The lower watershed contributes the majority of the sediment and nutrients during both dry and average water years, the one caveat being that during dry years the lower basin becomes a nitrate sink.

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Land Use and Water Quality on California’s Central Coast: Nutrient Levels in Coastal Waterways

University of California, Santa Cruz (UC Santa Cruz) | July 17th, 2003

Summary

Increased focus on addressing non-point source (NPS) pollution throughout the U.S. has raised awareness of agriculture’s impact on water quality. Growers are being a

Increased focus on addressing non-point source (NPS) pollution throughout the U.S. has raised awareness of agriculture’s impact on water quality. Growers are being asked to voluntarily limit the effects of their operations on adjacent waterways through programs such those initiated by county Farm Bureaus. If pollution cannot be voluntarily controlled, growers may face mandatory regulatory actions in the future. Maintaining water quality is an ongoing challenge in the Monterey Bay watershed, where industry, urban development, and farming all affect sensitive waterways. Excess nitrogen and phosphorous, herbicides, insecticides, and sediments that end up in sloughs and wetlands surrounding Monterey Bay have compromised water quality, contaminated shellfish, birds, and other wildlife, and generated unsafe levels of nitrate in drinking water. Although nutrient contamination is well recognized, to date there have been few efforts to link water quality with land uses such as urban development and farming in the region. To determine the way that land uses affect nitrogen and phosphorous concentrations in central coast waterways, researchers Marc Los Huertos, Lowell Gentry, and Carol Shennan have monitored water flow and sampled water quality in the Pajaro River and in other Pajaro Valley and Elkhorn Slough watershed creeks and agricultural drainages, for the past two water years (October 2000–September 2002). The research takes place through the UC Santa Cruz Center for Agroecology and Sustainable Food Systems (the Center) and is part of a larger U.S. Department of Agriculture grant awarded to Center director Shennan. This water quality monitoring program was developed in cooperation with the Santa Cruz County Farm Bureau, local Resource Conservation Districts, and other groups. We are particularly interested in the concentrations of two nutrients, nitrogen (nitrate-N) and phosphorus (ortho-P, also known as soluble reactive phosphorus), that are components of non-point source (NPS) pollution originating from urban and agricultural land uses.

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Land Use, Pollutants, and Water Quality in California Streams

California State Water Resources Control Board (SWRCB) | April 12th, 2012

Summary

A number of spatial patterns were evident in this survey of watersheds from throughout California. Stream sediment concentrations of heavy metals, such as cadmi

A number of spatial patterns were evident in this survey of watersheds from throughout California. Stream sediment concentrations of heavy metals, such as cadmium, copper, lead and zinc, tended to be highest in urbanized Los Angeles and San Francisco Bay area watersheds. Metal concentrations in sediments from San Leandro Creek (SF Bay area), Ballona Creek and San Gabriel River (Los Angeles area) were among the highest in the state. These metals are released to the environment from brake pads, plumbing, industrial and commercial activities. Industrial organic compounds such as PCBs (banned since the 1970s), PBDEs (flame retardants) and PAHs (hydrocarbons) were also generally highest in stream sediments from the Los Angeles and San Francisco Bay areas, though high concentrations were also measured in some more remote locations. In contrast to this urban pattern, mercury concentrations were highest in sediments from watersheds where it is geologically abundant and historically mined, though some urban streams also had relatively high mercury levels. The persistent legacy pesticide DDT was found in stream sediments from most urban and agricultural watersheds, where recent soil disturbance from development and tillage likely mobilizes DDT residues from applications more than 40 years ago. Pyrethroid pesticides are increasing in use in California and were detected in 55% of the samples statewide (51 of 92). The highest pyrethroid concentrations were measured in sediments collected from urban watersheds, plus two agricultural watersheds along the central coast. Approximately one quarter of the sediment samples collected were significantly toxic to amphipods, which are resident crustaceans representative of important aquatic food web links. Of these samples, 6.5% were identified as highly toxic. The highly toxic samples were collected from agricultural watersheds in the Tulare basin and central coast, in urban areas of southern California, and in the Tijuana River. Other toxic samples were collected from a wide range of watershed types, including those along the north coast, the Tahoe area, and urban and agricultural areas across the state. On a statewide basis, watersheds with greater than 10% urban land cover had consistently higher sediment pollutant concentrations and toxicity than did watersheds characterized by agricultural or other land cover types. Metals, industrial compounds, DDTs, and pyrethroid pesticides were all found at significantly higher concentrations in urban streams. This pattern is evident at the statewide level, but other local and regional studies have previously shown that pollution levels and toxicity can be strongly related to agricultural and other land uses in specific areas. This is because the “agricultural” land use category used in the SPoT analysis is comprised of many different types of crops and farming practices, and the amount of polluted runoff from these lands varies depending on the types of practices employed.

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