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Agriculture & Water Quality in California

Monitoring water quality in a Central Coast stream.Over 400 different crops are produced in California, including more than a third of the vegetables and two-thirds of the fruits and nuts grown in the US, contributing more than $50 billion to California’s economy (California Department of Food and Agriculture). In 2020, the National Agricultural Statistics Service estimated that 24,300,000 acres of land in California are used for agricultural production. Agriculture is one of the few economic sectors that uses the natural environment as a production base, and some negative impacts on the land and water result from food production practices. Agricultural activity is among the leading contributors of sediment, nutrients and pesticides to rivers, streams, lakes and wetlands.  

Contaminants from agricultural activity are generally considered nonpoint source pollution, unless they come from a well-defined source, for example a pesticide mixing area. As irrigation and stormwater runoff moves off fields and farms, natural and human-made pollutants are picked up and carried away by the water, and are then deposited into lakes, rivers, wetlands, and coastal waters. Dissolved pollutants from farmlands can be carried through the soil into groundwater, where they may present hazards for human health if that water is used as drinking water. In much of California, elevated nitrate in groundwater presents such a hazard. For more information on nitrate in groundwater, visit these resources: Water Education Foundation's brief overview, "Addressing Nitrate in California's Drinking Water" report from UC Davis, and the State Water Resources Control Board's Nitrate Project.

The cumulative effects of small amounts of non-point source pollution from large areas of production create unique management challenges and may be harder to address than point source pollution such as may occur in manufacturing or accidental spills. Gradual changes in water quality may incrementally impair the ability of rivers, lakes and estuaries to support beneficial uses such as drinking water, habitat for diverse wildlife and recreation.

In addition to contributing sediment, nutrients, and pesticides, agricultural runoff may contribute salinity, increased water temperature, disease-causing microorganisms (pathogens), and naturally occurring metals to waters in the state. These contaminants may originate from runoff from cropland, animal lots, processing facilities and other common agricultural activities.

Examples of agricultural activities that can lead to negative water quality impacts.

Nonpoint Source Pollutant

Agricultural Land Use

Agricultural Activity That May Contribute



Tillage, especially on steeper slopes; irrigation or stormwater runoff


Animal access to waterways, Grazing that results in bare soil


Runoff from roads, Forest harvest activities

Nutrients (Nitrogen, Phosphorus)


Fertilizer, manure or other soil amendments; Irrigation or stormwater runoff



Pesticide application, Lack of containment for storage and mixing spills



Saline irrigation water, long-term history of irrigation, and lack of non-saline water to flush salts from soil; Application of manure, compost or fertilizer


Rangeland or irrigated pasture

Animal access to waterways; Irrigation when fresh manure is present


Animal access to waterways; Irrigation when fresh manure is present

Water temperature

Cropland, Rangeland, Forestland

Lack of vegetative cover along riparian edges

NRCS Role in Water Quality
Impacts from agricultural activities on surface water and ground water can be minimized by using conservation practices that are adapted to a specific site. Conservation practices can be structures, planted vegetation, or management techniques that help to improve or maintain the quality and quantity of water, soil, air, plant, and animal resources. For example, a farm owner or operator with soil erosion problems may choose to change how they manage irrigation water, plant grasses along the edges of the farm as “filter strips” to catch sediment in farm runoff, and build a sediment basin to reduce the amount of sediment that leaves the farm and enters a nearby stream. NRCS conservation practices are evidence-based and applied to specific situations to meet unique conservation challenges.

A California stream impacted by algae.The NRCS works with individuals, groups, and units of government to develop and implement conservation plans for private lands. A conservation plan by the NRCS provides a professional analysis of a landowner or manager’s natural resources (soil, water, air, plants and animals). First, the NRCS conservationist listens to the landowner’s goals and objectives for the farm operation and for resource conservation on the farm. Then, an inventory of the natural resource conditions on the farm is produced, including information like the soil types and soil characteristics, the slope and slope lengths of each field, crop types and rotations, and other data necessary to understand a farm’s soil and water quality and farm productivity. Then NRCS helps the landowner or manager craft a conservation plan based on their goals and budget. The plan includes conservation practices selected and designed for the specific farm. The landowner or manager then chooses the parts of the plan that work best for them and their operation. Once the conservation plan is completed, the landowner or manager can apply for financial assistance programs through NRCS to implement the plan. NRCS provides specific practice design(s) and technical guidance to the landowner or manager as the conservation practices are applied to the operation. 

California’s Agricultural Water Quality Regulations
Agricultural producers can use conservation planning and conservation practices to respond to water quality regulations. Water quality objectives and laws are set by the national Clean Water Act of 1972 and California's Porter-Cologne Water Quality Control Act. The US Environmental Protection Agency (EPA) administers and enforces the Clean Water Act, and in California delegates some of its authorities to State Water agencies.

Water quality in California as regulated by the Porter-Cologne Act is under the jurisdiction of the California State Water Resources Control Board (SWRCB) and the nine Regional Water Quality Control Boards (RB) which decide the standards, objectives, and beneficial uses for the waters in their region.  Both the SWRCB and the RBs are regulatory in nature.

Point sources and nonpoint sources of water pollution are regulated differently, and until the early 2000’s agricultural activities in California had a blanket waiver from water quality regulation. That changed in 2003 with the implementation of the Irrigated Lands Regulatory Program (ILRP)  / (PDF link). Although each Regional Board has a different approach to their ILRP, private agricultural land owners now must: 1. Monitor surface water for agricultural pollutants, whether individually or regionally through grower coalitions; 2. Complete farm evaluations that describe conservation efforts on each farm; 3. Have management plans in place for sediment and erosion control, irrigation water management, and nitrogen management; and 4. Test drinking water wells on agricultural parcels for nitrate contamination. In the Central Valley a stakeholder-led process to develop plans to address salinity and nitrates from activities on irrigated lands (Central Valley Salinity Alternatives for Long-Term Sustainability or CV-SALTS) began in 2006, and plans are beginning implementation in 2021.

In 2014, California passed the Sustainable Groundwater Management Act (SGMA) / (SGMA Groundwater Management) which is the first law to regulate groundwater use and quality statewide in California. This legislation has created a new system of local agencies called Groundwater Sustainability Agencies (GSA) which are charged with developing and implementing Groundwater Sustainability Plans (GSP) to reverse or prevent degradation of groundwater resources. SGMA is jointly enforced by the California Department of Water Resources, which is focused on water supply and management, and the Water Boards.

Water Quality Assessment
Man-made structures may influence the quality of a stream.Water quality assessments are important in determining the condition of the state’s waters. Government agencies, water quality coalitions, community and volunteer groups all monitor and maintain records. One of the most widely known water quality assessments is the “303(d) List”, which refers to water bodies that have water quality impairments by one or more pollutants or conditions. (A link to this data is below.) Information gathered from sources like this can be combined with professional judgment and field experience of conservation planners and landowners or managers to ensure that conservation practices contribute to the correction and prevention of water quality problems. Understanding water quality information and applying this knowledge to conservation planning helps landowners and NRCS conservation planners achieve the water quality improvements on private lands.

Agriculture & Water Quality Data

  • U.S. Geologic Survey (USGS)
    The National Water Quality Assessment (NAWQA) Program was established to address where, when, why, and how the Nation's water quality has changed, or is likely to change in the future, in response to human activities and natural factors.  From 1991-2001, the NAWQA Project conducted interdisciplinary assessments and established a baseline understanding of water-quality conditions in 51 of the Nation's river basins and aquifers, referred to as Study Units. NAWQA activities during its second decade (2002-2012) focused in large part on national and regional assessments. These assessments built on continued monitoring and assessments in 42 of the 51 Study Units completed in the first decade, with an emphasis on synthesizing the results of the Study Unit investigations on major water-quality issues such as pesticides, nutrients, volatile organic compounds, ecological stream health, and trace elements.
  • US Fish & Wildlife Service
    National Wetland Inventory map Wetlands Mapper ( is designed to deliver easy-to-use, map-like views of America’s Wetland resources. It integrates digital map data along with other resource information to produce current information on the status, extent, characteristics and functions of wetlands, riparian, and deepwater habitats.

U.S. Environmental Protection Agency (EPA)

  • How’s My Waterway? was designed to provide the general public with information about the condition of their local waters based on data that states, federal, tribal, local agencies and others have provided to EPA. Water quality information is displayed on 3 scales: community, state and national.
  • Water Quality Data Portal  The Water Quality Portal is the nation's largest source for water quality monitoring data. The Water Quality Portal (WQP) uses the Water Quality Exchange (WQX) data format to share over 380 million water quality data records from 900 federal, state, tribal and other partners.
  • WATERS GeoViewer The WATERS GeoViewer tool is an EPA GeoPlatform based web mapping application that provides access to spatial data sets, watershed level reports linked data information, interactive upstream / downstream search capabilities, interactive watershed delineation, and underlying EPA GeoPlatform items that can be used to create other mapping applications.

State of California

  • My Water Quality - If you’re wondering: Is our water safe to drink? Is it safe to swim in our waters? Is it safe to eat fish and shellfish from our waters? Are our Aquatic eco systems healthy? Is there regional monitoring data near me? This site will show you maps and data to help answer those questions.
  • California List of Impaired Waters (“303(d) List”) - Access an interactive map of impaired water bodies in California, which can be searched by the water body name, location, and/or pollutant of interest. The 303(d) report is available here, which provides details on the water body, the pollutant or stressor causing the impairment (such as temperature or nutrients), the potential sources of the pollutant (such as municipal or agriculture), and the estimated size of the water body that is impacted.
  • Groundwater Ambient Monitoring and Assessment Program (GAMA) The GAMA Groundwater Information System consists of groundwater sampling data and water level information. An interactive Google-based map displays water quality data from various sources and is searchable by chemical or location.
  • Nitrate Impacted Water Wells - This interactive tool is intended for private domestic well owners to evaluate if their well is near a nitrate-impacted well. The map interface displays the location of wells with known test results above the nitrate maximum contaminant level (MCL), and allows a user to enter an address to see if a nitrate-impacted well is within 2,000 feet.
  • SWAMP  The Surface Water Ambient Monitoring Program (SWAMP) is the only statewide program tasked with assessing water quality in all of California’s streams, lakes, wetlands, estuaries, and coastal waters. SWAMP coordinates State and Regional Water Board monitoring throughout the State, and is in a unique position to collaborate with partner organizations to produce timely information through reports, fact sheets, websites, and an extensive water quality database – all targeted to support water resource management in California.

Tools for Water Quality Assessment
During the conservation planning process, an NRCS planner may use different methods, or “tools”, to assess the quality of water or the threats to water quality on a farm or ranch. Some of the most commonly used methods are:

  • Stream Visual Assessment Protocol: Provides a simple procedure to evaluate the condition of a stream based on visual characteristics. It is designed for use by landowners and conservationists in the field. The protocol provides an overall assessment of the condition of the stream and riparian ecosystems, identifies opportunities to enhance biological value, and conveys information on how streams function and the importance of protecting or restoring stream and riparian areas. The assessment can be completed in 15 to 20 minutes and no prior training in biology or hydrology is required. 
  • Windows Pesticide Screening Tool (WinPST) combines site-specific soils data with pesticide information and farm conditions to estimate the risk of pesticide loss from a farm. The same tool is available to the public through the UC IPM website. Look for the “Protect Water” button within each Pest Management Guideline page. 
  • The Nitrogen Hazard Index is a tool developed for California that uses soil, crop, and irrigation information to estimate relative hazard of nitrogen loss to groundwater from a field. This tool is under revision at this writing (2021).
  • The Nitrogen Index (pdf link) was developed by the USDA-Agriculture Research Service (ARS) with other partners. It is a tool that can be used to quickly calculate the risk of nitrogen movement from farming systems into the environment. The Nitrogen Index integrates data on a series of management practices, weather conditions, soil characteristics and off-site factors. It compares the effects of different management practices on nitrogen losses and distinguishes practices with high and very high risk levels from practices with medium, low and very low risk levels. 
  • The California Phosphorus Index is a tool designed to evaluate risk of P loss from individual agricultural fields to water bodies of concern for P pollution. The P Index is not designed to estimate the quantity of P lost from the field. The P Index can estimate risk of P loss under current management and management after a conservation plan is implemented. Access this tool from the NRCS Field Office Technical Guide (Choose "California”, then use the Document Search tab and keyword search for “Phosphorus index”).
  • The Revised Universal Soil Loss Equation (RUSLE2models soil erosion from farm fields under different scenarios and helps a user to compare practices that will reduce erosion and improve soil health on their farm. This tool only estimates sheet and rill erosion from the farm field and is not suitable for estimating concentrated erosion (such as gullies) or estimating sediment loading to streams.

Agriculture and Water Quality Planning

Water Quality Training


Wendy Rash, State Water Quality Specialist
Phone: (530) 792-5633



Updated: 06/09/2021