BAY DELTA PLAN: State Water Board adopts initial biological goals for the Lower San Joaquin River

The biological goals will inform adaptive implementation methods for flows, evaluate the effectiveness of implementing the Lower San Joaquin River flow objectives, and inform future changes to the Bay-Delta Water Quality Control Plan.

At the September 6 State Water Resources Control Board meeting, Board members took another step forward in the long-running effort to update the Bay Delta Water Quality Control Plan (or Bay-Delta Plan) by unanimously approving initial biological goals for the Lower San Joaquin River.  Erin Foresman, Environmental Program Manager, led the staff presentation.

As a framework for protecting beneficial uses in the Bay-Delta watershed, the Bay-Delta Plan establishes water quality objectives and outlines a comprehensive plan for their implementation.  However, despite the requirement to review and update the Plan at least every three years, this has only occurred three times since the first plan was adopted in 1978.  The most recent revision dates back to 2006, and efforts to update it have been in progress since 2009.

Given the size of the watershed, which includes the Sacramento and San Joaquin Rivers, the Board is working on the update in two phases: Phase one encompasses the Lower San Joaquin River and Southern Delta salinity standards; Phase two will be the Sacramento River and interior Delta flows.

In December 2018, the State Water Board adopted new and revised flow objectives for the Lower San Joaquin River and its salmon-bearing tributaries, the Stanislaus, Tuolumne, and Merced Rivers.

  • The new and revised numeric flow objectives apply from February to June and require 40% of unimpaired flow with an adaptive range of 30-50% on each of the Stanislaus, Tuolumne, and Merced Rivers at the flow gauge closest to the confluence with the Lower San Joaquin River. Foresman explained that unimpaired flow refers to the flow production of a water basin unaltered by diversion of streams or imports and exports to a watershed and is essentially an estimate of the water supply available for instream and consumptive uses.
  • The minimum base flow objective applies on the lower San Joaquin River at Vernalis and requires flows of 1000 cubic feet per second (CFS) with an adaptive range of 800 to 1200.

The Bay Delta Plan includes a program of implementation, which outlines the broad strategy for achieving the objectives and reasonable protection of beneficial uses.  The program of implementation for the Lower San Joaquin River flows requires the State Water Board to complete several additional actions, including establishing the Stanislaus, Tuolumne, and Merced (STM) Working Group to assist with the implementation of the Lower San Joaquin River flow requirements and the development of biological goals to assess the effectiveness of new and revised flow objectives.

The Bay Delta Plan requires the development of biological goals for lower San Joaquin River salmonids; biological goals for other species may be developed in the future.  Biological goals are quantitative metrics that will inform adaptive implementation methods for flows, evaluate the effectiveness of implementing the Lower San Joaquin River flow objectives, and inform future changes to the Bay-Delta Plan.  Biological goals are not intended to assess individual water rights holders’ compliance with the Bay Delta Plan.

The Bay Delta Plan requires biological goals to be developed for abundance, productivity, genetic and life history, diversity, population spatial extent distribution, and structure, all metrics of viable salmon population concepts or VSP.  The biological goals must be science-based, consistent with legal requirements, and SMART (Specific, Measurable, Achievable, Results-focused, and Time-bound).   The biological goals were developed based on recommendations from a 2019 Independent Science Advisory Panel report and similar efforts to develop biological goals, including the Bay Delta Conservation Plan and the Collaborative Science and Adaptive Management Program.

The goals will be reassessed at least every five years and as additional information is collected using an adaptive management approach.  In addition, as the Board improves engagement with Tribes and environmental justice groups, the biological goals will be modified as necessary to incorporate traditional ecological knowledge and other relevant information.

The staff then discussed the specifics of the biological goals and how they were developed in great detail.  (See 4:35:00 – 4:53:00 )

Tina Cannon Leahy acknowledged that there is litigation pending in Sacramento Superior Court regarding the Lower San Joaquin River and Southern Delta Salinity Standards update to the Bay-Delta Plan.  The Superior Court has coordinated 12 cases together under the name “State Water Board cases.” An entire week of oral argument was recently heard on the cases, with six additional days scheduled.

Four comment letters on the draft biological goals were received from parties to the State Water Board cases, raising some legal and technical issues.

“The Office of Chief Counsel has reviewed the legal issues in these letters and found that they do not have merit,” said Ms. Leahy.  “These issues include but are not limited to allegations that the Board should not or cannot act because litigation is pending; that the board’s approval of biological goals requires the California Environmental Quality Act or CEQA review, that the biological goals are somehow an amendment to the Bay Delta Plan, or that the board’s approval of biological goals is an alleged underground regulation.”

“The Board may act today,” she continued.  “Even though the litigation is pending, there is no court order preventing you from taking action to approve the initial biological goals.  As explained in whereas paragraph nine, approving the biological goals, which are metrics that the Board can use to assess progress, is not a project within the meaning of CEQA, and that is explained in the resolution.  The biological goals do not amend the Bay-Delta Plan; they were required by the Bay-Delta Plan.  In addition, the biological goals are not an underground regulation.  They are not a rule or standard of general application in the legal sense of those words.  Finally, to the extent that parties are reraising issues currently being litigated in the Sacramento Superior Court right now, this board meeting is not the proper forum to debate them.”

As a result of the comments received, staff had two changes to the proposed language.  The first is to clarify that the evaluation of the effectiveness of voluntary agreements would be subject to the specific provisions or terms of any voluntary agreement as may be approved in any future updates to the Bay-Delta Plan and not the biological goals.  The second is to improve the clarity in describing specifically what the Board is approving.


The Board then heard from the public.  There were eleven commenters, a mix of irrigation districts and NGOs.

Peter Drekmeier with the Tuolumne River Trust pointed out Central Valley salmon are on the brink of extinction, and there’s no more room for compromise.  “We need to aggressively restore habitat, and higher flows are the key ingredient. … During the recent three-year drought, unimpaired flow on the Lower Tuolumne River between February and June averaged just 13%.  I realized this has been a long process developing the biological goals.  My sense is you’re probably going to approve them.  But we need to look at strengthening them and making the priority be the restoration of the salmon-based ecosystem that the Pacific Coast depends on.”

John Buckley pointed out that there has been a lack of meaningful action since the Board adopted the update, and it’s time to move forward.  “It’s not enough for the Water Board and Department of Fish and Wildlife to continue to express desirable intentions that don’t result in meaningful actions.  The current version of the biological goals still has flaws and perhaps can be improved, but my key comment today is it’s time for adoption, not further delay.”

Cynthia Cortez with Restore the Delta said the timeline, as expressed in the biological goals, risks there being no spawning salmon or fish left in the waterways to protect.  She noted the closed fishery season this year demonstrates the impacts that decreased fish populations have on communities, as Tribal communities and Delta communities depend on thriving fish populations for cultural practices and sustenance.

Julie Zimmerman with The Nature Conservancy said they support the adoption of the biological goals by the Board at this meeting.  Still, they have recommendations for strengthening the goals to be consistent with plan objectives.  She then had several specific technical comments on the biological goals and how they must be strengthened to be consistent with plan objectives.

Ashley Overhouse with Defenders of Wildlife also expressed support for the Board to adopt goals today but said the biological goals must include goals for juvenile Chinook salmon survival in the main stem of the San Joaquin River and that those goals must be considered in determining adaptive adjustments to updated flow standards.

Jon Rosenfield with the San Francisco Baykeeper pointed out the biological goals were meant to be considered 180 days after the adoption of the updates.  “I would suggest that if the board wants to fulfill the intent of the Bay Delta Plan updates and see more collaboration and exchange in the STM group established by those updates, the board should move forward expeditiously with implementing the flow updates while there are still wild spawning salmon, steelhead and other native fishes on those tributaries to protect.”

He also pointed out the lack of a biological goal for chinook salmon survival in the main stem of the San Joaquin.  As a result, the biological goals provide no guidance for adaptive management or future plan updates for conditions in the main stem San Joaquin River as it enters the Delta, which is inconsistent with the purpose of the plan updates and the viability objectives.  The abundance goals still do not reflect a statement consistent with attaining the salmon doubling objective.

“In sum, although the current draft biological goals still do not reflect what the Plan or POI needs to accomplish to be considered a success.  Staff have made important and valuable improvements.  We appreciate their efforts.  It’s time for the Board to adopt these initial goals, emphasize the need for continued improvement, and move forward with implementing the updated flow standards, which are now long overdue.”

“Some goals are better than none,” said Brett Baker, attorney at Nomellini Grilli & McDaniel and counsel for the Central Delta Water Agency.  He pointed out that the goals focus exclusively on chinook salmon and ignore other species of concern that use the Delta estuary.  He noted the effects of selenium on the development of splittail in the San Joaquin River.  “When we increase deliveries, the quality of the water that comes down to San Joaquin suffers due greatly to the embedded toxins in the soil in some of those areas where they’re delivered, and also due to the fact that we exclude the Friant and San Luis and Upper San Joaquin River and Kings River from some of these flow standards and flow requirements.”

Cindy Meyer with the San Luis Delta Mendota Water Authority supported the comments made by the State Water Contractors, especially the need to amend the draft resolution and the report specifically acknowledging that the biological goals are not regulatory requirements and will only be used to assess the long-term trends.

Tom Berliner with the Merced Irrigation District said there’s a water rights issue.  “The resolution states that addressing water rights is an essential part of the Bay Delta Plan and meeting the biological goals.  However, as you know, there has not been any water rights proceeding.  And the entirety of the responsibility and the damages to be realized by our constituents have been pinned on the irrigation districts and the SFPUC.  The Plan ignores downstream water users on all of the tributaries and the San Joaquin River.  And those parties not only divert water, but they certainly have impacts on the quality of the water and the timing of flows and should be taken into account.”

Mr. Berliner said the twelve years for implementation is simply not enough, as it doesn’t consider the multiple events that can impact success, such as drought, flood, fires, climate change, and other impacts on water quality, as well as ocean harvests and migration success.   He wanted the Board to delay their vote until all the Board members’ questions and concerns were addressed.

Michael Cook with Turlock Irrigation District had technical and legal concerns with the biological goals.  Tuolumne River partners have requested the State Water Board amend the resolution to include specific language that clarifies the biological goals do not apply to those parties that have entered into a voluntary agreement with the State Water Board.  “The change sheet does make it clear that the voluntary agreement will be evaluated by the standards in the voluntary agreement.  But it doesn’t make clear that the implementation of the Bay Delta Plan is a voluntary agreement or the biological goals, not both at the same time.”


After some minor changes and clarifications to the resolution, the Board unanimously approved the resolution and the initial biological goals.

This article first appeared in Maven’s Weekly Water Blast, the newsletter for donors and sponsors of Maven’s Notebook.  Become a donor or sponsor of the Notebook and exclusive water news and more in your inbox every Monday morning.

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