An aerial view of the John E. Skinner Delta Fish Protective Facility, located two miles upstream of the Banks Pumping Plant, contains behavioral guidance devices, known as louvers, that divert most fish away from the pumps that lift water into the California Aqueduct. At the Skinner Fish Facility, up to 15 million fish a year are saved from the pumps and returned to the Delta. Florence Low / California Department of Water Resources

DPIIC: The CVPIA and the state’s Incidental Take Permit: Ecosystem-based Management in the Delta

The Delta Stewardship Council established the Delta Plan Interagency Implementation Committee (DPIIC) after the adoption of the Delta Plan in 2013.  The Committee is comprised of high-ranking members of 18 state, federal, and regional agencies who meet at least twice a year to coordinate programs and projects that affect land, wildlife, and water resources in the Delta.  At the July 2020 committee meeting, members heard presentations on the Central Valley Project Improvement Act and the state’s new Incidental Take Permit for the State Water Project and how those programs utilize principles of ecosystem-based management.


US Fish and Wildlife Service Regional Director Paul Souza began the agenda item by acknowledging that the Central Valley Project Improvement Act is an important program that has invested millions of dollars in on the ground projects to benefit salmon and the ecosystem of the Delta and its watershed since its passage in 1992.

Dan Castleberry, Assistant Regional Director, Fish & Aquatic Conservation at the US Fish and Wildlife Service recalled that one of his first permanent positions with the service was to help build the approach to implement the fish aspects of the Central Valley Project Improvement Act.

We were trying at that point in time to take an ecosystem-based approach to implementation,” said Mr. Castleberry.  “That structure then became a foundational element for the Cal Fed Bay-Delta Program, pulling in a lot of the staff from the agencies that were working to implement the Anadromous Fish Restoration Program into the Cal Fed Bay-Delta Program.  It was identified as a ‘Category A’ program in the Cal Fed ROD, which essentially integrated the anadromous fish aspects of the CVPIA into the Cal Fed Bay-Delta Program.  And it has continued on to this day.”

The one thing I wanted to emphasize is that from my point of view, having worked on anadromous fish in the Central Valley for close to 40 years, without the Central Valley Project Improvement Act efforts, mostly on the mainstem Sacramento and tributaries to the mainstem Sacramento but throughout the watershed, we might have well lost winter-run chinook salmon and spring-run chinook salmon as we went through drought periods and other challenges to those species,” he continued.  “I think, through the CVPIA and with the help of our multiagency partners, we’ve done much to sustain the production of all of the native anadromous species in the system.”

Overview and brief history of the Central Valley Project Improvement Act

Next, David Mooney, Deputy Area Manager for the Bureau of Reclamation’s Bay-Delta Area Office, and Donald Ratcliff, Central Valley Supervisor of Fish and Aquatic Conservation for the US Fish and Wildlife Service, gave an overview and brief history of the Central Valley Project Improvement Act, some of the major accomplishments for fisheries, and how the Department is shifting their actions and evaluations that were developed during the formative years of the program.

The restoration plan for the Anadromous Fish Restoration Program was built by folks all throughout the Central Valley that had probably the best information and the brightest minds at the time and we’ve been dutifully trying to implement for over 20 years to where we are now,” said Mr. Ratcliff.  “We’re looking at those actions and evaluations and changes through time and try to maximize our investment, to make sure we have the science to understand where we should continue to invest and move forward with the program.  We’ve been working in an ever-changing environment for 20+ years and we have some big wins, but we’ve also got a long way to go in a lot of different places.”

The Central Valley Project Improvement Act was passed by Congress in 1992.  The Act had a number of different aspects to it, including a number of provisions on water contracting and water management that changed operations of the Central Valley Project.

While the focus for this presentation is on the fishery resources, Mr. Mooney also noted that there are other components to the program, such as providing firm and reliable water supplies to over 19 local, state, and federal wetland habitat areas or refuges, and the Independent Program that focuses on primarily on terrestrial species and potentially even non-listed fish.  The program has a modeling program and also supports the San Joaquin River Restoration Program and the Trinity River Restoration Program.

The majority of the funding for the program comes from the Central Valley Project Restoration Fund which is funded by the Project water contractors and power customers.

The Central Valley Project Improvement Act is a large, complex program with activities in 28 of the watersheds from Lake Shasta all the way down into Bakersfield and including the Delta.  There are eight active fish provisions with six at or near completion.

The CVPIA rededicated a portion of the Central Valley Project yield to be operated for fish and wildlife purposes, as well as instream flow programs and other management programs.

The program has done a lot of work on various facilities, such as the Tracy Fish Facility for salvage of fish that would otherwise enter the pumps, the Temperature Control Device at Shasta Dam, replacing the Red Bluff Diversion Dam with a pumping plant, and fish screens throughout the Central Valley, such as the Contra Costa Fish Screen and other facilities, including non-project facilities.

There are separate programs for Clear Creek habitat restoration and spawning and rearing habitat for Central Valley Project watersheds.  The program also monitors adult escapement and juvenile production and has far-reaching influence on a lot of Reclamation’s activities.

From 1992 to 1997, folks worked to figure out how to implement the CVPIA and the fisheries program, which has a goal to achieve the doubling of anadromous fish populations from historic levels form the 1960s through 1992 when the CVPIA was passed.

The overarching idea for the plan was based on the best science of the time and the best understanding of the systems and impacts from the Central Valley Project and the State Water Project.  It included all kinds of various individual actions throughout multiple watersheds in the Central Valley, representing what folks believed were the best actions and evaluations that could be taken that to help the program reach the doubling goal.

The idea is the doubling of natural production – not just numbers of fish in the system,” said Mr. Ratcliffe.  “It’s a long-term and sustainable doubling of natural production of all the runs of chinook salmon, steelhead, white and green sturgeon.  Initially there were stripers and American shad, although stripers have been struck from the language since.”

The final restoration plan was drafted in 1997 and finalized in 2001.  It identifies programs, provisions or tools, and the principles and approaches to use those tools to address what was considered limiting factors.  There were 289 actions and evaluations that were prioritized from high to medium to low priority throughout the watersheds.  Those actions varied from large and broad-reaching actions, such as screening all of the diversions in a watershed, to site-specific actions such as fish passage or loss of spawning habitat.  There were evaluations to broad issues like entrainment of fish throughout all the tributaries as well as evaluations of site-specific issues.

Major accomplishments of the Central Valley Project Improvement Act (CVPIA)

Over the past 25 years, the program has had major accomplishments: the Shasta Temperature Control Device, the ‘gates up’ operation of Red Bluff Diversion Dam and construction of the large screening facility there, installation of the Contra Costa Fish Screen, improvements to the Tracy Fish Collection Facility operations, and studies to ensure that as projects are implemented, they are performing as expected.

The program has restored habitat on both CVP and non-CVP streams, including in-channel, floodplain, and rearing areas; gravel augmentation; fish passage projects; and juvenile and adult monitoring under the assessment and monitoring program.

One of the large successes of the Central Valley Project Improvement Act program has been at Clear Creek, a CVP stream in Northern California, where they were able to address many of the limiting factors for the entire watershed.  The removal of Seltzer Dam in 2000 opened up the upper part of Clear Creek with better habitat and cooler temperatures for the benefit of salmon and steelhead, especially the spring-run chinook.  The program continues to work on habitat, recontouring the profile of Clear Creek, allowing it to meander and act more naturally as it enters the river, instead of being channelized through an area of heavy mine impact.

What we’ve seen from that is fish numbers have gone up, both for fall run and for spring run, and because we have that passage, good habitat, reasonable control, and the ability to work with the water even in drier years,” said Mr. Ratcliff.  “We’ve seen a very resilient system that, even as some of the other streams that have seen populations increase in the 92 era on have struggled to maintain those increased numbers of production through drought and other issues, Clear Creek tends to be very resilient in comparison in both the fall run and spring run populations.”

Mr. Ratcliff noted that they aren’t here to present that the CVPIA has done this all on their own.  “This is work done with a lot of our partners, not only the funding and the projects that we’ve been able to implement but the relationships we’ve made and the people we’ve been able to work with and the funding we’re able to leverage to really work on larger-scale watershed approach to make sure we’re addressing all the limiting factors, monitoring these fish, and collectively leveraging funding and momentum to do as much as we can, and not just as a standalone program.”

Through the 1990s, Butte Creek was the focus of a major fish passage program that had many agencies and multiple sources of funding and addressed a large number of upstream passage issues for adults as well as downstream issues related to diversions and screening to protect juveniles.

Basically that watershed went from a few hundred spring run in decent years prior to implementing a lot of those actions to many thousands of spring run in many years now,” said Mr. Ratcliff.  “It has faced some challenges.  A lot of us view it as resilient, still maybe not as resilient as Clear Creek.  There are certainly concerns in dry years that our spring run in Butte Creek are challenged.  But huge investments by CVPIA and many of our other partners have allowed us to be a lot more sure that in most years, those fish can get through the system, get into the proper habitat, successfully spawn and rear, and we’ve seen great returns on natural production.

Throughout the Central Valley, the CVPIA has completed a wide array of habitat restoration projects: in-channel, side channel, and floodplain rearing habitat projects.  The slide on the lower left shows examples from the Mokelumne and Merced Rivers.  On some of the projects, they were able to reclaim mine tailings and use materials on-site rather than trucking it in, which puts the appropriate size gravel back in the river, create these floodplains, and get rid of the mine tailings.

We’ve done a wide range of those types of projects all the way from just trucking gravel in and putting it in and letting the river sort it out to these fairly highly complicated floodplain and in-channel habitat restoration sites that are a little more holistic,” Mr. Ratcliff said.

The program has also completed numerous fish passage projects throughout the Central Valley where possible.  The slide shows three examples of sites where they have implemented projects that both improve upstream adult passage but also is protective of juveniles heading downstream.  Numerous projects like these have been implemented.  These projects include channel-spanning instream rock ramps, boulder weir type facilities, traditional fish ladders, replacing low water crossings with concrete box culverts to create a bridge, and other smaller-scale fish passage projects that are very effective.

Looking to the future

Since the program’s inception, the CVPIA program has implemented a number of great projects at a high cost.  “We’ve seen some really successful spots within certain watersheds, but we know there’s a lot to be done throughout the valley,” he said.  “We’re continuing to do our best to maintain populations.  We haven’t made the moves towards the doubling goals that we would like for a lot of the watersheds, certainly with some exceptions such as Clear Creek, Butte Creek and a few others.”

Based on an independent review in the mid-2000s of the program, they shifted to looking at the science that underlies their decision making, the projects that are implemented, and how they are monitored in a formal adaptive management framework.  They use ‘adaptive resource management’ which is an iterative version of adaptive management supported by decision support models.

In 2015-16, they started the CVPIA Science Integration Team which is open to all who are interested in fish and aquatic habitat to have a place to come to bring their science, to bring their ideas, and help build and refine models to incorporate current data to make the best decisions possible.

With these models that we’ve built, it allows us to develop quantitative hypotheses with testable hypotheses and get measurable outcomes, and predict what our projects will do hopefully to continue to make the best choices possible based on science and not necessarily just based on a list that we developed and have tried to implement through time,” said Mr. Ratcliff.

With respect to the CVPIA and the Delta, Mr. Ratcliff said Delta is a high priority since before 1997 when initial efforts were underway to put CVPIA into action.  The CVPIA has worked closely through the years with many different restoration programs, including Cal Fed Bay-Delta.

We’re at a place now where we’ve worked for many years to develop some pretty robust models, especially for fall-run, continuing with winter and spring run as we have some time to work forward, but modeling the Delta continues to be a challenge,” he said.  “We haven’t done a lot of projects in the Delta through CVPIA outside of some of the major water infrastructure things that Dave talked about.  The same is true with a lot of our modeling efforts, understanding how the Delta works exactly and how the fish we’re interested in following from the tributaries that we’ve worked so hard to produce and protect fare as they go to the Delta.  That is a place where we need help to be able to make the best decisions.”

We understand that the structured decision making efforts currently going on throughout the Delta as well, and so we feel like we’re at a place where we’re understanding the system better as a whole and we need to be doing a better job of bringing our science to the table and integrating it with that of others and sharing with others,” said Mr. Ratcliff.  “Things don’t just get affected as they travel downstream, the watershed is a whole watershed, and maybe a lot of us have worked in small parts of it, but we should never pass up a chance to integrate those things.”


This item began with Department of Water Resources Director Karla Nemeth announcing that Dr. Lenny Grimaldo, a scientist with over 20 years experience working in the Delta, has recently come on board with the Department as the Assistant Director for Environmental Services; his job will be implementing the state’s new Incidental Take Permit for the State Water Project.

This is really the first time that we have had a standalone California ESA permit,” said Ms. Nemeth.  “It is a new endeavor for the Department and orders of magnitude more effort, but we’re all really excited about it.  We’re really excited about the strides that we can make in adaptive management and monitoring and really carrying on these discussions in a public way so we can share with the public what we’re learning as we go.”

Overview of the Incidental Take Permit (ITP)

Lenny Grimaldo then dove into some of the details of the Incidental Take Permit (or ITP).

The permit is for ten years and covers four species under the California Endangered Species Act.  They will be coordinating with Reclamation to protect those species that are also federally listed, such as salmon, steelhead, and green sturgeon.  There is an adaptive management program and the potential to be integrated with the voluntary agreements, should they come to fruition.

He acknowledged there are some key differences between the state’s incidental take permit and the federal biological opinions.  He gave few details but indicated that for the most part, the differences lie in the decision making structure process, thresholds for salmon, and spring export curtailments.

The project area for the permit is smaller than the CVPIA’s in that it is mostly limited to the legal Delta, and Suisun Marsh and the Bay.

The project facilities include only the State Water Project facilities in the Delta and Suisun Marsh.  This includes the Skinner Fish Facility, the Clifton Court Forebay, the South Delta Barriers Program, the operations of the migration barrier at Georgiana Slough and Barker Slough, and the Roaring River Distribution System.

Real-time operations


What I particularly like about pieces of this permit is this commitment to real-time operations of Old and Middle River (OMR) management,” said Dr. Grimaldo.  “I have published a few papers on Delta smelt and OMR.  I worked on it quite a bit for the 2008 biological opinion for the FWS and we’re so much farther ahead in our understanding of how real-time operations work and the potential effects on endangered species.  Some of the commitments in this permit are integrated variable pulse protection, which is related to the first flush dynamics; we know that often we see a lot of fish that get salvaged right when it starts to rain.  There are protections for when salmonids start to enter the Delta and there are enhanced protections for longfin smelt when they do occur in the area.”

The permit incorporates real-time operations for species that are listed in the permit.  They also have to have close coordination with the operations group, both for the state and the federal projects.  There’s also a commitment to continuing participation through WOMT, weekly risk assessments for operational advice, and to develop salvage forecast models.

We have a gob of data from the salvage facilities,” said Dr. Grimaldo.  “A lot of us have been working on these forecast models.  Wouldn’t it be neat to have this interactive online tool where everyone can go and look at real-time conditions and predict what our salvage would be for that week?  The permit allows for some sort of development towards that process.  I love that because what it does it is takes the faith-based management out of consideration and it really relies on the history and what we know about how entrainment is influenced by different environmental conditions.”

Habitat restoration and mitigation requirements

The permit also includes habitat restoration and mitigation requirements.  The permit carries over the targets for restoration and mitigation that were identified in the 2008 opinion for Delta smelt.  Currently, the Department has about 7900 acres under construction or planned, and the permit also calls for an additional 396 acres of tidal marsh habitat for Barker Slough Pumping Plant.

The longfin smelt habitat restoration and mitigation requirements were carried over from the 2009 incidental take permit, and Dr. Grimaldo said they already have 590 acres credited.

The Tule Red restoration project breached the levee this past fall, and right before he came to DWR, he and his team went into the marsh to do research and they found a lot of longfin.

This is exciting as this is showing that some of these restoration sites are going to work and they’re going to work well,” said Dr. Grimaldo.

He then made a pitch for doing more focused research to see how are these fish using these sites, moving beyond the food web.  “I want to know are they growing better, are they moving in just for spawning, and are there spawning habitats in there.  Science questions like that that I really want to push our group forward with because the ultimate metric that your site is working well is to actually see these endangered fish on the site.  So I’m excited to say, Tule Red, it’s already working.  The fact that we’ve got gobs of longfin in there is pretty cool.

There are other mitigation requirements.  One of them is the Yolo Bypass Big Notch project, which has the objective of improving the migration corridor for salmonids and other native fish and restore access to floodplain habitat.  Dr. Grimaldo noted there is a lot of research that shows that native fish benefit when they have access to floodplains.  It is an important project involving many agency partners and is well underway to getting implemented with key permits submitted already.

Commitment to adaptive management

This is going to require close coordination within and outside the Department, he said.  They will be working closely within the Department as well as with the Department of Fish and Wildlife.

We want to be on the same page,” he said.  “How we’re implementing this, defining the different permit conditions, and we’re working on that process as we speak.  I think the key part of that is the adaptive management implementation.  Working with them, working with Reclamation on how are we going to go about implementing of our permit, and to be mindful of the tough questions that we need to answer for the effectiveness of these different conditions as well.”

The permit also calls for an adaptive management process to address scientific uncertainty.  “It’s no secret that the permit is currently under litigation, and I’m not going to discuss that now, but at least there’s a way that we can resolve and bridge the gap with some of these key questions that we have on how these conditions are going to affect our endangered species,” he said.  “Through this process, we get to interact with our agency partners and the contractors.  Maybe we’ll expand this membership, but the idea is to develop this structured decision-making process for tackling those tough questions.”

Commitment to new science

There will also be new science that comes out of the permit for Delta smelt and longfin smelt, food web research, new science for winter-run and spring-run chinook salmon, and new research facilities.  There is a commitment to support the existing IEP long term monitoring program and monitoring programs such as the Enhanced Delta Smelt Monitoring (EDSM) that provides a lot of information on not only the Delta smelt but longfin and chinook salmon as well.  The permit allows for reviews of the monitoring programs, so they can look at surveys to see if they should be expanded and how in order to get the information needed to better inform real-time operations and assessment.

The permit calls for the review of a summer-type action which they have already begun setting up how the review will proceed.  “We’ve already seen some promise with this habitat action,” said Dr. Grimaldo.  “We’ve seen potential evidence of changes salinity as well as other metrics that we care about, and what we’re going to do is continue to set up how we do this study in a way that will effectively allow us to decide what sort of features of the action we may want to adjust or alter based on the performance of how it occurs over the next couple years.”

The permit also makes an overall commitment to science and looking at how the project affects salmon and the smelt.  For salmon, for example, there’s a call for monitoring plans that look at the potential effects of water transfers, particularly in the Feather River, a new and ongoing commitment to develop a spring run JPE, additional salmon science requirements, pathology, monitoring, rearing habitat in the Bay-Delta, the spring run life cycle model, and an entrainment prediction tool.

The permit commits to enhancing understanding of longfin smelt tick and calls for an expansion of monitoring, including expansion of the smelt larval survey and entrainment monitoring.

We’re just getting started on developing the longfin smelt science program charge, and I’m really looking forward to seeing how that process unfolds,” said Dr. Grimaldo.  “We have a lot of questions that the permit calls for us to evaluate in this four year review, so I’m pretty excited that we get to do that and to improve our knowledge of longfin smelt in the system.”

One of the things they want to do is develop a new life cycle model, which is one way they can test the effectiveness of the actions in terms of the permit, as well as climate change and how the species is responding overall in the environment.  They also want to complete the longfin lifecycle in captivity, characterize some of their spawning habitat and microhabitat, and get a better understanding of what factors may affect when adults move into the Delta and when juveniles exit the Delta.

Finally, there’s a commitment to funding the Rio Vista Estuarine Research Station with the permit calling for 66% of the funding required.  Dr. Grimaldo said the idea is to consolidate the IEP staff into one facility as the hub for conducting science in the Delta.


Lead Scientist Dr. John Callaway noted that the science program is coordinating a workshop in early September on spring-run chinook salmon science to identify knowledge and data gaps for spring run and inform the juvenile population estimates for the Central Valley spring-run in the Sacramento Valley.  It will be held online three half days on September 8-10.  (Click here for more information and to register.)

Dr. Callaway also agreed that the joint funding proposal for science definitely has been successful, and following on that success, the Delta Science Program is working on the initial phases of a solicitation with the Bureau that probably will come out late this year or early 2021.  They are hoping to have a regular competitive opportunity for research for science in the Delta.

US FWS Regional Administrator Paul Souza emphasized that the federal government is in consensus on the importance of the Rio Vista Estuarine Research Station.  “It took us a few years to figure out how to grow Delta smelt, quite frankly.  It was probably 3 or 4 years before we could make that work, so my question is, how close are we to being able to grow longfin smelt?  Have we figured out that biology?

Dr. Lenny Grimaldo said that the longfin smelt is different than the Delta smelt; the science shows they hatch 2-3 psu and not in freshwater like Delta smelt.  “I understand the culture facility has been using a little saltier water in their rearing, and apparently they are doing pretty well.  That’s preliminary information, and I think that’s something we’re going to have to look at.  Longfin smelt have different requirements than Delta smelt, so maybe it’s feeding as well.  I think we’re making progress there.”

What I’m noticing with this meeting is this community of resource managers and scientists are very dedicated to collaborating and working together,” said Delta Stewardship Council Chair Susan Tatayon.  “I think Dan Castleberry and Lenny Grimaldo are two examples of the history of collaboration and the caring for achieving the doubling goal and other objectives.  I just wanted to note that there is a spirit of collaboration, and as Dan said, when we collaborate and get rowing in the same direction, amazing things can happen and the science as we’re moving forward is magnitudes beyond what we saw in the 1990s.”

The Department and DWR are working very closely in the implementation of this and looking at issues of integrating with both the biological opinions and their implementation and particularly highlighting the importance of the adaptive management program for the Department in the structure of the permit,” said Carl Wilcox, Delta Policy Advisor for the Department of Fish and Wildlife.  “That allows us as we go forward to make changes in an organized way based on new information that comes in as part of a structured process that relates both to the status of the species but also to the health of the estuary and how the species respond to it.

Chair Susan Tatayon noted that both the CVPIA and the ITP presentation discussed not only real-time monitoring but structured decision making and forecast models.

Dr. Lenny Grimaldo said with respect to structured decision making and forecast models and how they can inform ecosystem management, he said, “Those things take courage.  For example, if you want to test a forecast model, you have to take the courage to say, ok well, maybe we’re going to do things a little differently this time.   Perhaps for this group, we could have a shared commitment to that courage. … There are situations where you have a model that provides a result and you test whether that result met your expectations, then you change your models.  But the bottom line to move forward with those sorts of tools.

Dr. Callaway noted that there has been a lot of progress made on integrated modeling efforts in the Delta, and suggested an update would be appropriate at an upcoming DPIIC meeting.

During the public comment period, the question was asked, what voluntary agreements the ITP is being integrated with, and is there any VAs at this point?

The state is continuing to meet with various tributary stakeholders about the framework that the state put out in late January, and we are looking at several tributaries – the Tuolumne, the Mokelumne, the Yuba, so that’s one set of issues,” said DWR Director Karla Nemeth.  “Then, separately, we are also in communication with our federal colleagues around how we might merge some differences between the biological opinions and the California ESA permit and the voluntary agreements.”

Now obviously the biological opinions and the incidental take permit under CESA, those have a different dimension because there’s litigation on all sides of both of those permits,” she continued.  “But certainly in our incidental take permit, there is language that relates to the voluntary agreements, particularly how we approach spring outflow issues and how we generate those flows and understand those flows and their purpose, so in that sense, specific to the incidental take permit and the VAs, there is a degree of potential interaction between those things should the voluntary agreements be completed over the course of the next months or year or so.”

If you haven’t seen it, I’d refer you to page 18 or 19 in the actual state’s permit,” said Chuck Bonham.  “The permit does a smart job of building the space for alignment between these proceedings to kind of resolve and integrate with each other.  The permit could have been silent on all of that … very positive conversation, it rejected the idea of being siloed and instead purposefully allows for future integration.”


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