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

Harmful Algae (Elsevier) | February 17th, 2017

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.

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

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.

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

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.

Land Use, Pollutants, and Water Quality in California Streams

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

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.

Managing a cyanobacteria harmful algae bloom “hotspot” in the Sacramento – San Joaquin Delta, California

Journal of Environmental Management (Elsevier) | December 10th, 2023

Nitrate Implementation Measures Study (NIMS) Final Report

Central Valley Salinity Alternatives for Long-Term Sustainability (CV-SALTS) | March 31st, 2016

This report summarizes the Nitrate Implementation Measures Study (NIMS) which addresses nitrate contamination in the groundwater basins underlying the floor of the Centra

This report summarizes the Nitrate Implementation Measures Study (NIMS) which addresses nitrate contamination in the groundwater basins underlying the floor of the Central Valley and appropriate implementation measures to mitigate nitrate contamination for these areas using a phased approach that includes providing safe drinking water, reducing or eliminating impacts to drinking water sources and implementing managed restoration activities where needed to restore beneficial uses in groundwater. These implementation measures will be incorporated into the SNMP. The findings from both the SSALTS and the NIMS will be used to guide discussions regarding the need for changes to the existing Basin Plan to facilitate salt disposal and mitigation measures for nitrate in a manner that is most beneficial to the region covered by the SNMP. 

Nitrogen Fertilizer Loading to Groundwater in the Central Valley

University of California, Davis (UC Davis) | October 31st, 2017

Nitrate‐nitrogen is the most common pollutant found in the Central Valley aquifer system of California. This project provides a long‐term assessment of past and curr

Nitrate‐nitrogen is the most common pollutant found in the Central Valley aquifer system of California. This project provides a long‐term assessment of past and current potential nitrogen loading to groundwater on irrigated and natural lands across the entire Central Valley of California using a nitrogen mass balance approach; assesses the long‐term implications for groundwater quality in the Central Valley (Sacramento Valley, San Joaquin Valley, and Tulare Lake Basin); evaluates potential best management practices to reduce groundwater nitrogen loading from irrigated lands; and provides a planning tool to better understand local and regional groundwater quality response to specific best management practices and policy/regulatory actions. The project complements other work to assess the vulnerability of Central Valley groundwater to nitrate contamination, sources of nitrate in groundwater, and how to reduce source loading.

Nitrogen Tracking and Reporting Task Force: Final Report

California Department of Food and Agriculture (CDFA) | December 6th, 2013

Agriculture in California is highly diverse in terms of food production, crop management, ecosystems, and climate. Nitrogen fertilizer is essential for crop food producti

Agriculture in California is highly diverse in terms of food production, crop management, ecosystems, and climate. Nitrogen fertilizer is essential for crop food production. Nitrogen fertilizer use over several decades in California has led to nitrates in groundwater. Recognizing that nitrates from agricultural nitrogen fertilizing materials have entered some California groundwater systems used for drinking water, CDFA convened the Nitrogen Tracking and Reporting Task Force in 2013 as part of a multi-pronged administration effort to address nutrient management and water quality. This Task Force was charged with implementing Recommendation 11 of several recommendations made to the Legislature by the State Water Board: “CDFA, in coordination with the Water Boards, should convene a Task Force to identify intended outcomes and expected benefits of a nitrogen mass balance tracking system in nitrate high-risk areas. The Task Force should identify appropriate nitrogen tracking and reporting systems, and potential alternatives, that would provide meaningful and high quality data to help better protect groundwater quality.” This charge was achieved through several measures including, among others, understanding and discussing the pros and cons of existing nitrogen tracking and reporting systems, identifying desirable components or elements of existing systems and evaluating the variability and complexity of California agriculture in relation to where existing systems have been implemented. Through several meetings, presentations by subject matter experts and discussion, the Task Force members came to general agreement on several components of an effective nitrogen tracking and reporting system. The recommended system addresses eight key topics including: (1) System Structure; (2) Data Elements; (3) Roles, Responsibilities and Data Accessibility; (4) Benefits of Participation; (5) Verifiability; (6) Societal Benefits of the Recommended System; (7) Limitations and (8) System Phase-in. This report presents the Task Force’s discussions and recommendations including intended outcome and anticipated benefits of such a tracking and reporting system for nitrogen use.

Nutrient Fluxes from Sediments in the San Francisco Bay Delta

Estuaries and Coasts (Springer) | January 1st, 2014

In September 2011 and March 2012, benthic nutrient fluxes were measured in the San Francisco Bay Delta, across a gradient from above the confluence of the Sacramento and

In September 2011 and March 2012, benthic nutrient fluxes were measured in the San Francisco Bay Delta, across a gradient from above the confluence of the Sacramento and San Joaquin Rivers to Suisun Bay. Dark and illuminated core incubation techniques were used to mea- sure rates of denitrification, nutrient fluxes (phosphate, ammonium, nitrate), and oxygen fluxes. While benthic nutrient fluxes have been assessed at several sites in northern San Francisco Bay, such data across a Delta–Bay transect have not previously been determined. Average September rates of DIN (nitrate, nitrite, ammonium) flux were net positive across all sites, while March DIN flux indicated net uptake of DIN at some sites. Denitrification rates based on the N2/Ar ratio approach were between 0.6 and 1.0 mmol m−2 day−1, similar to other mesotrophic estuarine sediments. Coupled nitrifica- tion–denitrification was the dominant denitrification pathway in September, with higher overlying water nitrate concentra- tions in March resulting in denitrification driven by nitrate flux into the sediments. Estimated benthic microalgal productivity was variable and surprisingly high in Delta sediments and may represent a major source of labile carbon to this ecosystem. Variable N/P stoichiometry was observed in these sediments, with deviations from Redfield driven by processes such as denitrification, variable light/dark uptake of nutrients by microalgae, and adsorption of soluble reactive phosphorus.

Nutrients in the Nation’s Streams and Groundwater: National Findings and Implications

U.S. Geological Survey (USGS) | September 1st, 2010

A comprehensive national analysis of the distribution and trends of nutrient concentrations in streams and groundwater from 1992 through 2004 is provided by

A comprehensive national analysis of the distribution and trends of nutrient concentrations in streams and groundwater from 1992 through 2004 is provided by the National Water-Quality Assessment (NAWQA) Program of the United States Geological Survey (USGS). Findings describe the distribution and causes of varying nutrient concentrations in streams and groundwater throughout the Nation and examine the primary sources that contribute to elevated concentrations. Results show that excessive nutrient enrichment is a widespread cause of ecological degradation in streams and that nitrate contamination of groundwater used for drinking water, particularly shallow domestic wells in agricultural areas, is a continuing human-health concern. Finally, despite major Federal, State and local non-point-source nutrient control efforts for streams and watersheds across the Nation, USGS trend analyses for 1993–2003 suggest limited national progress to reduce the impacts of non-point sources of nutrients during this period. Instead, concentrations have remained the same or increased in many streams and aquifers across the nation, and continue to pose risks to aquatic life and human health. This Fact Sheet highlights selected national fndings and their implications, and serves as a companion product to the complete analysis reported in the USGS Circular titled “The Quality of Our Nation’s Waters—Nutrients in the Nation’s Streams and Groundwater, 1992–2004.”