San Joaquin River, South Delta.

DELTA INDEPENDENT SCIENCE BOARD: An update on the Bay-Delta Water Quality Control Plan

State Water Board staff provide an overview of the Bay Delta Plan and the progress to date

At the March meeting of the Delta Independent Science Board (ISB), in preparation for a potential ISB review of environmental flows, the Board was given on overview and an update on the progress to date on updating the Bay-Delta Water Quality Control Plan (or Plan.)  Erin Foresman and Matt Holland, both with the State Resources Water Control Board, provided an overview of the Plan’s progress to date, the two recent processes to update the Plan, the scientific basis used to support the updates, and how a potential ISB review on environmental flows can inform the State Water Board’s efforts.

The Bay Delta Water Quality Control Plan

Erin Foresman, an environmental program manager with the Division of Water Rights at the State Water Resources Control Board, began the presentation with a map of the Bay-Delta watershed showing the area covered by the Bay-Delta Plan.  This includes the entire San Francisco Bay, including the South Bay, Central Bay, and San Pablo Bay; it includes the estuary starting at the Golden Gate, moving east to Suisun and Grizzly Bays; and then the Sacramento San Joaquin Delta, and the tributary watersheds of Sacramento and San Joaquin rivers to the north and south respectively.   

The formal name of the Plan is the Water Quality Control Plan for the San Francisco Bay/Sacramento-San Joaquin Delta, or Bay-Delta Plan for short. 

The Plan was adopted according to requirements in the state’s Porter-Cologne Act and the federal Clean Water Act.  The Plan identifies and describes the beneficial uses of the waterways in the Bay-Delta, such as municipal, industrial, agricultural, water supply, fish and wildlife, and recreation, both contact and non-contact.  The Plan also includes narrative or quantitative water quality objectives intended to provide reasonable protection of those beneficial uses as required by the Porter-Cologne Act.  In the Bay-Delta Plan, those water quality objectives are primarily flow-dependent.

The Bay-Delta plan also includes a program of implementation, a broad strategy outlining the actions the Board can take to achieve the flow objectives.  Once the flow objectives are set, the objectives don’t implement on their own; the Board needs to take subsequent actions to require actions of individual entities, usually water rights holders, to bypass flows or make other operational changes to achieve a flow-dependent water quality objective.  The program of implementation also identifies non-flow actions by other agencies that can complement and reinforce the effects of the flow objectives.

The Bay-Delta plan also includes a section on monitoring and special studies.  There are two broad categories of monitoring required:  monitoring to demonstrate compliance with flow objectives and monitoring to help the Board assess if the flow objectives provide reasonable protection of beneficial use.  This information is used to evaluate the efficacy of the objectives and whether or not adjustments are needed.

Ms. Foresman noted that there are related water quality control plans that spatially overlap with the Bay-Delta Plan; the San Francisco Bay Regional Water Board has a basin plan that covers the San Francisco Bay watershed, and the Central Valley Regional Water Board has basin plans that cover the Sacramento River watershed and San Joaquin River watershed.

While there is overlap spatially, the Bay-Delta Plan addresses issues such as salinity, tidal and riverine flows that require control of water diversions, which are regulated through water rights,” explained Ms. Foresman.  “The San Francisco Bay, the Sacramento River, and San Joaquin River Basin plans address parameters such as toxic chemicals and other contaminants that are the maximum contaminant level-type of water quality issue.”

Implementation of the Bay-Delta Plan

The Bay-Delta Plan includes largely flow-dependent water quality objectives.  The State Water Board uses its dual authority with water quality and water rights to implement the flow-dependent water quality objectives.   Water rights decision 1641 (or D-1641) is a water rights order that implements portions of the Bay-Delta Plan by amending the water rights and licenses, in this case, of the State Water Project and the Central Valley Project.  

D-1641 assigns responsibility to the Department of Water Resources and the United States Bureau of Reclamation to modify diversions and other project operations sufficient to meet flow-dependent water quality objectives in the Bay-Delta Plan specifically to achieve Sacramento and San Joaquin River inflows, Delta outflows, and Delta salinity.  D-1641 also has requirements for State Water Project and Central Valley Project operations, such as gate operations and export limits.

Bay-Delta Plan review and updates

The Bay-Delta Plan is periodically reviewed and updated as required by both the Porter-Cologne Act and the federal Clean Water Act.  The Plan was first adopted in 1978 and has been updated several times, the most substantial of which was in 1995.

In 2009, the State Water Board began the process of reviewing and potentially updating flow-dependent water quality objectives in response to significant declines and lack of recovery of fish populations since the 1995 update.

In 2018, the State Water Board completed the first of the update processes by adopting new and revised flow objectives for the lower San Joaquin River and its three salmon-bearing tributaries for the reasonable protection of fish and wildlife beneficial uses.  The Southern Delta salinity objectives for the reasonable protection of agricultural beneficial uses were also updated.

The process to update flow-dependent water quality objectives for the Sacramento River, the Delta, and their tributaries is ongoing.

The general process to update and implement the Bay-Delta Plan is as follows:

    • The first step is to complete a periodic review of the Bay-Delta Plan to identify what issues should be further evaluated and what changes, if any, should be made to the Bay-Delta Plan. 
    • The next step is developing a scientific basis report to evaluate and document science and technical information that supports possible changes to the Bay-Delta Plan.
    • To comply with CEQA and the Porter-Cologne Act, a Substitute Environmental Document (or SED) is prepared.  Since the Water Board’s basin planning program is a certified regulatory program, the SED is prepared instead of an environmental impact report.  The SED also identifies the proposed amendments, evaluates alternatives, and discloses the environmental and economic impacts of making those changes or amendments to the Bay-Delta Plan.  The SED includes economic and other analyses not commonly part of an environmental impact report.
    • After the SED is prepared, the State Water Board considers whether to adopt the plan amendments at several public meetings where the proposed changes are presented, public comments are heard, technical analyses described, and questions answered as the Board has a conversation in public about the proposed Bay-Delta Plan amendments.
    • If the State Water Board adopts amendments or changes to the Bay-Delta Plan, they must be submitted to the Office of Administrative Law for approval before they can take effect.

Once approved, the State Water Board begins the process of implementing the changes.  There are three main tools to do so:

    • Adopt regulations;
    • Adopt a water rights order or decision; or
    • Put conditions in a water quality certification.

2018 Lower San Joaquin River and South Delta updates to the Bay-Delta Plan

In 2018, the Board adopted changes or amendments to the Bay-Delta Plan, new and revised objectives for the lower San Joaquin River and its three salmon-bearing tributaries, and revised southern Delta salinity objectives. 

Southern Delta salinity objectives

The amendments included a revision to southern Delta salinity objectives to protect agricultural beneficial uses, such as irrigation water in the southern Delta.  On the slide, the yellow dots and the half-green/half-yellow dot show the locations of the Southern Delta salinity compliance points.  The revised standard is 1.0 decisiemens per meter; the salinity objective is expressed as electrical conductivity and is a 30-day running average that applies year-round. 

The prior objective was a little bit lower; it was 0.7 decisiemens per meter from April through August; that was the irrigation season,” said Ms. Foresman.  “However, we revised the objective based on new technical information that demonstrated agricultural beneficial uses were still reasonably protected at higher salinity levels.”

San Joaquin River tributary flow objectives

The revised lower San Joaquin River tributary flow objectives apply from February through June.  There are two components:

  • For the tributaries, a percent of unimpaired flow that applies at the confluence or the mouth of the three salmon-bearing tributaries of the lower San Joaquin: the Stanislaus, the Tuolumne, and the Merced. Compliance is measured at the nearest flow station; the green dot on the map above shows on each tributary indicates where compliance will be evaluated.
  • A revision to the base flow objective on the lower San Joaquin River is measured at Vernalis, shown with the half green, half yellow dot.

The new tributary flow objective is expressed as a percent of unimpaired flow that will allow it to continuously adjust to a tributary’s specific hydrology, which can be extremely variable.  The prior flow objective was a fixed monthly average flow based on five water year types that applied to the San Joaquin River only for analysis.

The quantitative flow objective is 40% of unimpaired flow as a seven-day running average within 30 to 50% adaptive range.  The revised lower San Joaquin River base flow objective at Vernalis requires a minimum flow of 1000 CFS as a seven-day running average within an adaptive range of 800 to 1200 CFS.  Ms. Foresman noted the minimum flow objective is in place to provide protection in the very dry years in which 40% of unimpaired flow would not produce 800 to 1200 CFS at Vernalis.

The Bay-Delta Plan’s program of implementation identifies adaptive implementation options that allow for managing the required percentage of unimpaired flow as a total volume of water, or a water budget that can be released on an adaptive schedule where scientific information indicates a flow pattern different from that which would occur by tracking the unimpaired flow would better protect fish and wildlife uses, provided that the total volume of water is at least equal to the percent of unimpaired flow from February through June.

The adaptive implementation adjustments allow for using a functional flows approach to defining an alternative flow schedule subject to the budget constraint defined by the 40% of unimpaired flow,” said Ms. Foresman.

Schedule for implementation of the Lower San Joaquin River and Southern Delta salinity objectives

The slide shows a broad timeline for the actions needed to complete and implement the Lower San Joaquin River flow and southern Delta salinity objectives.  This winter and spring, draft reports describing biological goals and compliance methods will be released, and public workshops will be held to provide opportunities for stakeholders to provide feedback.   

The biological goals report describes the quantitative metrics used to assess the effectiveness of flow objectives, inform adjustments in flow schedules and required percent of unimpaired flow, and assess and inform future updates.  Compliance methods are numeric methods to evaluate and assess compliance with the unimpaired flow objective.  

Staff is working with DWR and Reclamation on a Southern Delta salinity operations plan, and a special studies plan to initiate CEQA for the implementation action.  The goal is to have the Board consider adopting biological goals, and the Executive Director consider approval of compliance methods by the end of summer 2022.  

From 2022 to 2023, if the Board moves forward with implementation as a regulation, the goal is to initiate CEQA and create a draft and final regulation for board consideration by the end of summer 2023.

Ms. Foresman noted there are other ways to implement, such as through a water right action.  While a decision on which pathway to take has not yet been made, this schedule would no longer apply if the Board decides to implement through a water right action as a water right decision would likely take longer.

Sacramento River/Delta flows update

Next, Matt Holland, a program manager in the Division of Water Rights at the State Water Board, discussed the update to the Sacramento River, its tributaries, the Delta, and the three tributaries to the east of the Delta.

Mr. Holland pointed out that there are many more tributaries in this part of the update than on the San Joaquin River.  “There’s a mix of regulated and unregulated tributaries,” he said.  “There are varying levels of water development on the different tributaries.  There are varying efforts at restoration on various tributaries.  So it’s a bigger and more varied set of tributaries than were included in the previous update.  And notably, it also includes the major reservoirs of the Central Valley Project and the State Water Project that are operated to meet water quality objectives in the Delta, and also to provide for the export of water from the Delta to the Bay Area, and the south of the Delta.”

He then discussed the potential elements of the Sacramento Delta update to the Bay-Delta Plan, noting that the Sacramento Delta Update is not as far along as the lower San Joaquin process.  There is also an active effort to develop a voluntary agreement to address the needs of the Sacramento Delta update.

He began with the new and modified inflow objectives being considered for the Sacramento River and its tributaries, and the Delta tributaries.  To date, they have been considering the objectives to be a percent of unimpaired flow, similar to those adopted for the San Joaquin River tributaries.  However, there is the possibility that in the context of a voluntary agreement, these might be blocks of water offered up by the various larger water users in the system that would be operated potentially flexibly to provide for functional flows.

The next category of objectives being considered are cold-water habitat objectives, which are intended to ensure that inflow objectives are implemented in such a way as to protect cold-water refugia below the rim reservoirs that block access to the natal spawning and rearing habitats of many salmonids.   Implementation can include actions such as reintroduction to restored systems such as Battle Creek, upstream passage, installation of temperature control devices, and other selective withdrawal means on dams.  This will be a narrative objective in the current proposals.

Also being considered are new and updated Delta outflow objectives.  If the inflow objectives are based on a percent of unimpaired flow, the outflow objectives would be designed to work with that inflow objective. 

Deer Creek, in the Lassen Foothills Conservation Area, a tributary to the Sacramento River. Photo by DFW

It probably would not be specific exactly a percent of unimpaired outflow, because we would also be protecting the inflows provided from the San Joaquin, and we may have different percentages of unimpaired flow in the San Joaquin and Sacramento basins,” said Mr. Holland.  “Additionally, if we’re implementing something more like a block of water approach from a voluntary agreement, we would have to design that outflow requirement to protect those blocks of water coming in from the other tributaries.”

The final category of objectives being considered are interior flow objectives.  These are things such as export constraints, such as the existing export/inflow ratio that limits exports from the southern Delta.  The objectives can also include operations of permanent gates or installation of temporary barriers that affect water quality and the routing of fish.

Changes to the program of implementation include both voluntary and default implementation paths.  This could include voluntary agreements or voluntary implementation paths for percent of unimpaired flow based on the objective.  The default implementation path would be a percent of unimpaired flow objective similar to the San Joaquin objectives that would track the percent of unimpaired flow through time.  It would also include compliance and effectiveness monitoring and reporting, as well as consideration of adaptive management measures.

With the voluntary agreements, there may also be other elements, including non-flow measures, such as habitat restoration actions or blocks of flow,” said Mr. Holland.

Scientific basis reports

The State Water Board is an agency in the California Environmental Protection Agency.  When a new regulation is adopted, the health and safety code requires the scientific basis for the regulation to undergo an independent peer review.  The statute requires specific features in that independent peer review, so an office within the State Water Board handles that to ensure that the statutory obligations are met. 

This aerial view looks north over the Middle River and the west levee – South Bacon Island Road.  Photo by Dale Kolke / DWR

The way that we’ve implemented this in the Bay-Delta Plan updates is to produce first a scientific basis report that starts with a problem statement,” said Mr. Holland.  “So, for example, we’ve seen long-term declines and failures of recovery of a number of native species and commercially important species in the watershed and flow alteration, and operations of water diversions contribute to those declines.  So we produce a scientific basis report that essentially reviews what the actions are in the State Water Board’s authority that could be taken and what would be the scientific basis for that suite of actions.

The scientific basis reports are produced, circulated for public comment, and ultimately peer-reviewed through an independent process.  Mr. Holland noted that the ISB’s role is valued because members of the ISB are selected for a broad perspective and are not participating in the system on a one-off basis.  So the Water Board has brought the scientific basis reports to the ISB for review.

I wanted to let you all know that collectively, the Independent Science Board has been a part of improving the products that we use to base our amendments to the Bay-Delta Plan,” he said.

After the science is documented to support the changes to the Bay-Delta Plan, the environmental and economic effects have to be further analyzed through the Substitute Environmental Document.  And then, the Board considers the information from that report in light of public comment and public process to arrive at some understanding of what set of actions constitutes reasonable protection.

“’Reasonable protection’ is the standard that the Board is obligated to meet,” he said, noting that a panelist spoke about the distinction between jeopardy and reasonable protection in a previous presentation.  “The Board is tasked with defining reasonable protection, which is not easy.  It’s a complex balancing act between various policy considerations, and it’s informed by but not dictated by technical and scientific information.”

Schedule for the Sacramento River and Delta flows update

He then presented a schedule for the Sacramento Delta update, noting that it was prepared for a board meeting in December.  Some things have yet to happen, such as the submittal of a proposed voluntary agreement.  However, he said they believe to be an aggressive but more or less achievable schedule for adopting the Sacramento Delta updates to the Bay-Delta Plan.

He said the State Water Board expects to receive a proposed voluntary agreement ‘any day now.’  Once received, they will develop a scientific basis report for the voluntary agreement through the summer of this year.  The process will include public review and comment and, ultimately, the required independent peer review.  The report will be sent to the ISB for review as well.  They expect to release the draft staff report (SED) for public review and comment in the fall and hold a public workshop next winter.

Then over the spring and summer of 2023, they will work to respond to comments and develop final proposed changes to the Bay-Delta Plan for the Board’s consideration in the late fall.

Mr. Holland acknowledged there’s always schedule uncertainty, but this is their best guess at the schedule right now.

How Delta ISB Review on Environmental Flows Can Inform Future Board Actions

With respect to how an ISB review on environmental flows can inform future actions of the Board, Mr. Holland noted that implementation actions on the Lower San Joaquin River and planning activities for the Sacramento Delta update are currently underway.  Those schedules are uncertain.  So, depending on how timing works out, there’s the possibility that the ISB would be involved in reviewing materials that are part of each of those processes.  However, the longer-term products are likely more useful on topics such as the efficacy of changed water quality objectives and a review of biological goals, he said.

If the ISB chooses to review environmental flows, Mr. Holland said there are some things to consider.

Aerial view of farmland and waterways in the Delta.  Photo by Dale Kolke / DWR

It’s important to understand the scope and complexity of the Water Board’s regulatory environment.  Besides the Clean Water Act, Porter-Cologne Act, and the water quality control plans, the Board has other water right orders and decisions that implement portions of the Central Valley Basin Plan.  For example, Water Right Order 90-5 addresses temperature management on the Sacramento River.  There are also water quality certifications and the state and federal Endangered Species Acts.  The Department of Fish and Wildlife administers stream alteration agreements that can address environmental flows.  There are also the Federal Energy Regulatory Commission flow requirements.

So there is a range of venues in which environmental flows are set at some level,” said Mr. Holland.  “And there are different balancing considerations that are taken into account in those different venues and different standards of protection.  So without becoming experts in all of those specific regulatory venues, I think it’s important to keep in mind that there’s a large universe of regulatory venues in which environmental flows are set and affected.”

They recommend that the ISB build on the existing scientific basis reports and other resources related to their planning activities, as well as the California Environmental Flows Framework.

We recommend that you focus on the role of scientific information in the intersection with policy, acknowledging that scientific information informs the policy decisions that are made but doesn’t dictate them,” he said.  “Any perspective you can bring on flexibility and implementing flexible flow objectives and evaluating their efficacy would be valuable to our processes, particularly in the future as we get into the nitty-gritty of implementing these things and evaluating them.”

The Water Board has authority to modify diversions and implement flow objectives, but we all understand that we need potentially more than just a modification of flows,” said Ms. Foresman.  “We also need habitat restoration and … the other ways that we can, maybe not the State Water Board, but other partners, provide habitat and flows that can amplify one another in terms of their biological response.”

The State Water Board has one clear regulatory authority, but it doesn’t necessarily have the other clear regulatory authority to compel habitat restoration,” she continued.  “But the way that the flow objectives were established for the San Joaquin River flows, it did try to provide room to make adjustments in those flow objectives if habitat restoration projects come online that are able to amplify the biological response, so that we can adjust without having to start the whole process all over again.   So that would be useful to consider.  And we’d be really interesting to hear Delta ISB viewpoints on that piece of it.”

Then, with respect to flexibility in flow objectives and adaptive management, it is monitoring intensive, and person-time intensive to make sure that we implement a certain flow objective where we’re doing the correct monitoring and we’re able to keep up with the cycle that we need to make adjustments as new information comes in.  So it would be interesting to hear Delta ISB feedback on all of those things.”


ISB Board Member Tanya Heikkila:  How do you see the California Environmental Flows Framework fitting in with the Bay-Delta Plan and the changes coming about?  Do you think it can inform how you think about updating the Plan?  Or do they talk to each other at all?

Matt Holland noted that the California Environmental Flows Framework began through another effort that is part of the Sacramento Delta update now, which focused on priority tributaries throughout the watershed, but mainly in the Sacramento basin.  “So staff working on that update were engaged with the Delta Science Program and requested a review of an approach to developing environmental flows for those priority tributaries.  That initiated a chain of events that resulted in the collaborations that led to the Environmental Flows Framework.  So it’s always been in parallel with our planning process.”

The Sacramento River at Fremont Weir.

I would suggest looking at our existing scientific basis report for the Sacramento Delta update,” he continued.  “It gets at this a little bit, at least in an implicit way, in the section that we wrote up on the development of environmental flows. … We included a review of various methodologies for developing environmental flows and arrived at the conclusion that the approach that we’re taking was attempting to be holistic and to provide for the ability to accommodate and include flow shaping to provide functions, but was also not intended to presume that we could identify all of the functions that flow is providing in the natural system.  I think of it as a little bit of humility with regard to our scientific understanding of how flow affects ecosystems.  So the way we’ve been trying to build flexibility in implementing a flow objective is, in principle, very compatible with the Environmental Flows Framework.”

I absolutely agree with your statement about compatibility and can use the Lower San Joaquin flow objective as an example,” said Ms. Foresman.  “The default flow objective is a seven-day running average.  It’s a 40% of unimpaired flow, and if you follow the unimpaired flow as it comes in, that’s kind of making functional flow decisions for you.  We’re just going to follow hydrograph as it occurs in nature, but it will be dampened because it’s a seven-day running average.

The adaptive implementation flexibility allows, instead of just tracking the unimpaired flow hydrograph on that seven-day running average, we can estimate the total volume of water that would come in from February through June,” she continued.  “We’ll be wrong at first, but we’ll get righter and righter as we get toward the end of the five-month period.  But we can use any means that we have to make decisions about a flow schedule that might work better than tracking the seven-day running average.  And if we have a very incised channel that only can have floodplain activation at 1000 CFS or higher, perhaps we want lower flows in the cooler months, something less than 40% of the unimpaired flow in February and March.  Maybe we took a little bit lower flow in February or March, and we want to invest that in a snowmelt simulation characteristic of the San Joaquin.  So we push that into those later months.”

It follows a functional flows concept,” she said.  “I’m not using the functional flow metric terminology of CEFF.  But you can blend those concepts and use the flow budget as your constraint.  And then, you can see how well you can meet the functional flow metrics.  So that’s a way that they can be blended, but I’m sure that’s not the only way they can be blended.”

ISB Board Member Dr. Lisa Wainger:  You presented a laundry list of goals and objectives in both of your talks.  It’s just not really clear to me how you balance all those.  You have some off-the-top things required by regulation, and then there’s some stakeholder engagement.  But what is the real process by which you meet all these various objectives?

The Porter-Cologne Act requires reasonable protection of beneficial uses,” said Ms. Foresman.  “We initiated a periodic review, recognizing that some beneficial uses may not be sufficiently protected,  specifically fish and wildlife beneficial uses.  That periodic review led to a scientific basis report that suggested potential updates to the water quality control plan that are then evaluated in a CEQA document; we don’t call it an EIR because we have to include additional analyses … an economic analysis and analysis to see if we are going to be able to provide reasonable protection of that beneficial use.”

That’s a really hard task; it’s not defined in code,” continued Ms. Foresman.  “What is reasonable?  The State Water Board has the discretion to figure out what’s reasonable at this moment in time and balance competing beneficial uses.”

We do an economic analysis to identify the economic impacts of adopting a different amendment.  So for the San Joaquin, we looked at 20% of unimpaired flow, 30% 40% 50% – we looked at all the different ranges, evaluated the economic effects, and provided that information to the Board.  And they looked at that and considered and weighed everything.”

South Fork of the Tuolumne RIver.

One thing we did see is that at 40%, of unimpaired flow, we did get a solid improvement in temperature profiles that would promote survival of Chinook salmon outmigrating juveniles.  We saw a very big benefit in more floodplain activation and an economic impact.  But when you go to 60% of unimpaired flow, for example, there was less improvement in temperature profiles and floodplain activation, but there was a substantially larger economic impact.  So that’s some of the information that the Board uses to make those balancing decisions.

For a given range of alternatives you might identify, even the technical information itself can indicate the various things you’re trying to protect are very hard to reconcile,” added Mr. Holland.  “So, for example, in the Sacramento Delta update, the range of flows that we identified in the scientific basis report to be considered in the subsequent analysis was 35 to 75%, of unimpaired flow from the tributaries.”

Now, when we modeled that using a hydrology and operations model, it was very challenging to maintain any level of water supply at 75%, of unimpaired flow, and it’s very challenging to maintain enough storage in some of those larger rim reservoirs to feel comfortable that we can provide for temperature control below those rim reservoirs,” continued Mr. Holland.  “At the 35% end of the spectrum, you basically don’t see any change in the hydrology and operations.  And so, that technical information can identify that these ends of the range aren’t workable, and maybe that’s sort of trivial information.  But it does point us to somewhere in the middle. … “

I think in a less formal sense, it’s the trade-off analysis that the Board members are doing through a policy lens,” he said.  “That policy lens includes, what are the effects on real people?  What are the effects on how much agriculture the state can support?  How does this interact with other major regulations that affect these same stakeholders, such as SGMA?  So they have to make a very hard policy decision based on  a mixture of primarily technical information.  So it’s physical modeling, biological modeling, and economic modeling, but also the input from the public as to how much pain they can tolerate in various sectors.”

Print Friendly, PDF & Email