WATER BOARDS: Update on the Central Valley Water Board’s Irrigated Lands Program

Much progress made on implementation of Order WQ-2018-0002

Runoff and other discharges from agricultural lands affect water quality by transporting pollutants including pesticides, sediment, nutrients, salts, pathogens, and heavy metals from cultivated fields into surface waters.  Groundwater bodies are also impacted by elevated concentrations of pesticides, nitrates, and salts.  As a result, statewide, approximately 510,000 acres of lakes and reservoirs and 9,500 miles of rivers and streams have been identified as being impaired by irrigated agriculture, with many also similarly impaired by pesticides.

Runoff from agricultural lands is a form of pollution that originates from a widespread area, such as agricultural fields or urban stormwater runoff, and is referred to as nonpoint source pollution.  The federal Clean Water Act doesn’t really have a permit program per se for nonpoint sources; instead, it has the Total Maximum Daily Load program, which mainly applies to surface water quality, but not really groundwater.  

Under the state’s Porter-Cologne Water Quality Control Act, nonpoint sources were first given a waiver or an exception; they did not have to obtain a permit.  However, that waiver program went away in 1999 when SB 390 was signed into law, requiring the Regional Water Boards to review their existing waivers and to renew or replace them. To comply with SB 390, the Regional Water Boards adopted Waste Discharge Requirements (or WDRs) or revised existing waivers to address agricultural discharges.

The Central Valley Regional Water Quality Board did adopt Eastern San Joaquin Agricultural General Waste Discharge Requirements (or WDRs) in 2012  which regulated discharges to groundwater from irrigated lands as well as surface water discharges.  In response, three timely petitions for review were filed with the State Water Board by Asociación de Gente Unida por el Agua, et al. (AGUA), the California Sportfishing Alliance and California Water Impact Network (CSPA), and the San Joaquin County Resource Conservation District, et al. (SJCRCD).  This ultimately led to the adoption of Order WQ 2018-0002, which authorized discharges from agricultural lands to waters of the state within the Eastern San Joaquin River Watershed along with a number of requirements for monitoring and planning, implementation and evaluation of management practices, and participation in various education and outreach events.

Sue McConnell is the manager of the Central Valley Board’s Irrigated Lands Regulatory Program.  At the September 15 State Water Board meeting, she gave an update on the implementation of Order WQ-2018-0002, hereafter referred to as the ‘petition order’.


The goal of the Irrigated Lands Program is to ensure that discharges from commercial irrigated land do not impact beneficial uses of the water.  The Central Valley Water Board’s Irrigated Lands Regulatory Program covers over 6 million acres of land, which is about 75% of the state’s irrigated land.  Activities on those lands are regulated using 9 general WDRs with the growers organized into 14 agricultural coalitions.

Seven of the general WDRs are geographically based. There is one WDR that is commodity specific for the California Rice Commission, which was exempted from the petition order’s nitrogen groundwater protection requirements because rice operations have unique cultural growing practices that minimize any potential discharge of nitrogen.  There’s also a general WDR for growers who choose to be regulated individually; currently, there aren’t any growers choosing that option right now. 

For the coalition-based WDRs, there is one coalition per WDR except for the Tulare Lake Basin Coalition, shown in blue, which has seven coalitions. Coalition-based WDRs contain requirements for the coalitions and their grower members.

The growers are ultimately responsible for compliance, first by obtaining coverage, and then by complying with the WDRs by implementing management practices that are protective of water quality and by preparing plans and submitting reports on those practices.  Grower plans and reports are template-based; some reports stay on farm and others are submitted to the coalitions who then compile the information and submit it to the water board.

Coalitions represent growers and assist their members by informing them of the requirements and letting them know what they need to do to comply with the WDRs.  They act as intermediaries between the growers and the water boards.

However, coalitions do not enforce the WDRs.  They don’t monitor or inspect individual member discharges or operations to determine compliance of individual members.  But while they don’t enforce the WDRs, coalitions do have responsibilities.

Coalitions are responsible for fulfilling regional requirements and addressing water quality issues by conducting water quality monitoring, and they’re working with growers to implement practices in accordance with management plans.  Coalitions must meet the requirements of the WDRs and cooperate with the water boards by providing the information needed to assess grower compliance and to proceed with enforcement on growers who are not complying.

The focus of the petition order was the East San Joaquin Coalition, which has about 700,000 irrigated acres and 3100 members.  The petition order updated the East San Joaquin general WDRs and included requirements for the Central Valley Water Board’s Irrigated Lands Program as well as the irrigated lands programs statewide.


The petition order was adopted in February of 2018.  In October of 2018, our Executive Officer approved three templates that were required by the petition order.  The templates were publicly noticed and comments were addressed, which is a process we follow for all new templates and other groundwater protection elements.  Two of the new templates focused on additional irrigation planning as well as irrigation and nitrogen management practice reporting.

The third template for drinking water notification was developed in close collaboration with environmental justice organizations, the Division of Drinking Water, and the agricultural coalitions.  It is a component of meeting the new drinking water well monitoring requirements as coalition members with drinking water wells that exceed the nitrate standard must provide this template to users to inform them of the nitrate concentration and the dangers of consuming that water. 

The template is sent to coalition members with an information packet prior to initiation of the monitoring requirement.  It’s also available on the Irrigated Lands website in English, Spanish, Punjabi, and Hmong.  Also a copy of the template must be provided to the Central Valley Water Board as documentation that users were informed.

The petition order required the East San Joaquin coalition members to start monitoring on-farm drinking water wells annually in 2019, and the Central Valley Water Board prioritized the monitoring timelines for the other coalitions based on groundwater nitrate concentrations.  In 2020, members of the seven Tulare Lake basin coalitions are required to monitor their drinking water wells annually; in 2021, three additional coalitions will begin the monitoring, and in 2022, members of the last three coalitions will start monitoring their drinking water wells.

The picture on the slide is a screenshot from GeoTracker, the State Water Board’s groundwater database, showing how the drinking water well data is displayed.  Each dot is a sample location; the grower information is not shown, only the nitrate concentration and the sample date.  The table on the right shows the sampling results as of a few weeks ago.  Ms. McConnell noted that the Tulare Lake Basin members have until the end of the year to sample and that only growers with wells used for drinking are required to monitor. 

In the form evaluations that are due next year, growers will be required to report if they have wells on their own parcels which will determine the total number of wells that need to be sampled.

For the East San Joaquin and the Tulare Lake Basin, the big coalitions that are prioritized for earliest drinking well monitoring, over 30% of the wells sampled did exceed the nitrate drinking water standard,” said Ms. McConnell.  “I want to stress that one of the highest priorities for the Irrigated Lands Program is ensuring that users are notified and they have that nitrogen information in hand when there is an exceedance.  Also, we will be incorporating CV-SALTS requirements in the irrigated lands WDRs to address replacement water.”

In February of 2019, the Central Valley Regional Water Board updated all of the coalition WDRs as mandated by the petition order.  “We didn’t take the five years that was allowed by the petition order to update our WDRs because earlier experience taught us that having coalitions on different timelines can cause confusion and disruption, so last February, the CVWB updated all coalition-based WDRs to align the coalition and most of the member requirements by 2021,” she said.  “The drinking water well monitoring effort was implemented by CVWB staff and will apply to all coalition members by 2022.”

In March of 2018, East San Joaquin Coalition members were required to start preparing Irrigation and Nitrogen Management Plans.  Members subject to management plans also worked with the coalition to develop and prepare Management Practice Implementation Reports (or MPIRs), which is another new template required by the petition order.

In July of 2019, the Executive Officer approved a methodology proposed by the East San Joaquin Coalition for identifying nitrogen efficiency outliers, a classification that can trigger additional certification outreach and management practice requirements.  In August, as required by the petition order, an external expert review of the East San Joaquin Coalition surface water monitoring framework was initiated.

The petition order required the external review to answer certain questions about the East San Joaquin Surface Water Monitoring Framework which included whether the representative monitoring approach was appropriate for regulating irrigated lands operations, whether the framework has sufficient density to reasonably identify exceedances throughout the watershed, and whether the framework provides adequate feedback between management practices implemented and water quality goals.

A stakeholder advisory group was formed comprised of three environmental, three agricultural, and three water board representatives.  That advisory group helped select and inform a five-member external expert review panel with the expertise that was specified by the petition order.  In January, the panel held a three-day meeting with a field trip to some of the East San Joaquin Coalition’s monitoring locations.  Ms. McConnell noted that the pandemic did delay the second meeting until the end of August.

The panel is now working on and will be providing draft written recommendations in October and plans to hold a meeting in November to receive feedback from stakeholders before finalizing their recommendations.  Irrigated lands staff will be bringing recommendations to the regional board next year.  Information on the expert panel review is available by clicking here.

So in March of this year, East San Joaquin Coalition members submitted Irrigation and Nitrogen Management Plans for the first time, and then in July, that information was used to submit field-level nitrogen applied over nitrogen removed (A/R) and management practice data with anonymous member ID. 

The petition order required the development of a groundwater protection formula to calculate values and targets for townships that are subject to groundwater quality management plan to achieve compliance with receiving water limits.  So also in July, the thirteen coalitions who were subject to the requirement jointly submitted a proposed groundwater protection formula workplan.  The coalition workplan proposed to use the Soil and Water Assessment Tool (or SWAT) in conjunction with grower reported data to estimate current nitrogen loading.  SWAT is a public domain model used to quantify impacts of management practices in large complex watersheds that is able to account for weather, land use, soils, slope, evapotranspiration, crop growth, irrigation nutrient loading, and other factors.  The workplan was released for public comment and the extended comment period recently ended.


This is the first annual report to the State Water Board as required by the petition order.  They will be reporting every fall on data received and the progress being made towards identifying effective practices and acceptable nitrogen applied over removed (A/R) ranges.  In 2022 and every two years after that, the report will include whether the anonymous field level data is sufficient for program oversight and determining progress.

Next March, farm evaluations will be due for all coalition members with a reporting frequency of every five years.  Nitrogen removed coefficients will be required for crops covering 95% of the irrigated acreage in the region.  Next spring, Irrigation and Nitrogen Management Plans will be due for all coalition members.  Management Practice Implementation Reports will be due for all members subject to management plans.

Also next spring, groundwater protection values will be due for townships that are in water quality management plans.  After Executive Officer approval, the groundwater protection formula will be used to estimate nitrogen loading due to current farming activities.  These groundwater protection values will be township based and incorporated into groundwater quality management plans within six months.  Those values will be released for public review and comment prior to approval.

In summer of 2021, the coalitions will be providing field level data on nitrogen applied over nitrogen removed (A/R) and management practice data by anonymous member ID.  They will also continue to provide township data.

The collection and evaluation of nitrogen management practice data are a key component of the irrigated lands effort to assess grower trends and performance,” said Ms. McConnell.  “The data are also used to identify protective management practices through the management practice evaluation program, identify nitrogen efficiency outliers, develop the groundwater protection targets, and establish acceptable ranges of A/R ratios by crop.  Given the importance of the data, we’ve been engaging with the coalitions on making sure that these member reported data are of the highest quality, and mostly coalitions have or are moving towards web-based reporting which is helping improve the data quality, but there’s still some work to be done.”

We’re also collaborating with UC Researchers on our shared interest of using that field level data to find correlations between nitrogen and management practices.  They are also looking at the quality of the data from the various coalitions.  We will of course be sharing the results of that collaboration as they become available.

In spring of 2022, the groundwater protection targets must also be developed for incorporation in groundwater quality management plans.  The groundwater protection targets are township-based nitrogen loading rates needed to achieve compliance with the objectives as required by the WDRs.  This requires information on existing water quality as well as a process for estimating the effect that the nitrogen loading has on groundwater.  Targets will be released for public review and comment prior to executive officer approval and reviewed every 5 years.


Patrick Pulupa, Executive Officer of the Central Valley Regional Water Quality Control Board, acknowledged the work of Sue McConnell and her team and meeting the fairly aggressive timelines for developing the expert panel, revising the programs, and revising the monitoring – and most of it done ahead of schedule.  He also said that the rollout of drinking well monitoring is going incredibly well. 

The big thing out there is still the unknown unknowns in terms of what the compliance numbers are, but in terms of getting wells sampled, it’s really been an incredible achievement,” he said.

Chair Esquivel noted that the growers and the coalitions are also involved in implementation of the Sustainable Groundwater Management Act and in CV-SALTS, and asked how can the science and technical work in the irrigated program benefit these other processes?  What are then the opportunities that we can do so we understand the complexity of the various authorities and take advantage of limited dollars in technical work around water quality and protection of it in the context of SGMA?

It’s no secret that there’s been a lot of critiques of the groundwater sustainability plans and that their water quality work has really taken a back seat to water quantity work,” said Mr. Pulupa.  “I truly think if you do solve the water quantity picture and you do have plentiful water banking and plentiful inundation of a lot of fresh water into these aquifers, you’re going to deal with a lot of the nitrate problems and you’re going to deal with a lot of the issues pertaining to water quality.  I think the critique generally has been, well what if that doesn’t materialize, what are the backstops there?  … Your teams are working through those issues with DWR.  Is the analysis in these GSPs robust enough to ensure that if it doesn’t rain or if the estimates of new sources of water don’t come through, what happens?  Maybe in that review, the dial gets turned back up for water quality.  Again, that’s something that we’ve been kind of tracking and trying to remain faithful to as we make sure that the data needs of all the programs are being met.”

Mr. Pulupa said that there’s a lot of coordination going on between the GSAs, between the management zones under CV-SALTS, and the irrigated lands coalitions. He noted that the coalitions are driving a lot of the initial management zone setup for CV-SALTS that’s happening right now.

It’s something frankly we were hoping for because it makes it a lot easier to manage and it also represents the coalitions taking ownership of the nitrate issues within their jurisdiction,” he said.  “You see that dynamic developing where the coalitions are merging and working within the management zone structure to deal with the water quality issues.  There is the parallel track of the water quantity issues being developed through the GSAs, which also have significant overlap although I think the players are a little different.”

Where the environmental justice and DAC folks come in, is that we’re seeing a pivot towards CV-SALTS and DAC engagement in the long-term solutions, I think largely because the feedback that we’ve been getting is that their voices haven’t necessarily been heard through the development of the GSPs and CV-SALTS represents another opportunity to be heard as more long-term solutions are being crafted for water quality at least within this domain.  Then there is the SAFER program and what benefits that will yield, where that program will work and won’t work, who has responsibilities for what.  The Irrigated Lands Program is at the intersection of so many of these programs.”

He said in terms of resources, he thinks they are doing exceptionally well but the burden is still pretty high.  “Policing these permits is incredibly difficult and a lot of staff hours have been spent making sure that the drinking water well program gets stood up and gets stood up appropriately, and so a lot of our effort has been placed in the past couple years, and rightly so, but we also recognize there are other areas of the program that have suffered because we have limited staff to accomplish that. … A lot of prioritization.  The baseline prioritization is who is drinking impacted water.  And I think that’s going to be our touchstone moving forward, certainly in CV-SALTS but also in the irrigated lands program.”

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