METROPOLITAN WATER PLANNING & STEWARDSHIP COMMITTEE: USFWS Regional Director Paul Souza explains the biological opinions

Paul Souza is the Regional Director of the Pacific Southwest division of the US Fish and Wildlife Service, which covers California, Nevada, and the part of Oregon that includes the Klamath Basin.  At the November meeting of Metropolitan Water District’s Water Planning and Stewardship Committee, Mr. Souza gave a presentation on the recently released biological opinions for the long-term operations of the Central Valley Project and the State Water Project.

He noted the importance of the Central Valley Project and the State Water Project in supporting 25 million Californians, urban centers like Los Angeles and the Bay Area, and some of the richest farmland in the world.  He also acknowledged there are very important environmental considerations as well.

When agencies such as the Bureau of Reclamation and the Department of Water Resources take actions that may affect threatened and endangered species, the federal fish and wildlife agencies will complete a review and produce a biological opinion.  The last time a biological opinion was completed for the Central Valley Project and the State Water Project was a decade ago, and Mr. Souza said they’ve learned a lot since then and they wanted to bring that best thinking into the latest review.

Fisheries get the headlines and for good reason,” he said.  “Salmonids are extraordinarily important for Californians and Delta smelt is a species that we’re entrusted with protecting and recovering.  Though I do want to make the point that water is critical for all kinds of wildlife and for the health of the environment broadly speaking, not the least of which is our national wildlife refuges which are critically important for the Pacific Flyway and for migratory birds of all kinds.”

They worked very hard during this consultation to come up with a plan that’s protective of fisheries and the environment, but also finds flexibility for water supply when possible, he said.  “I want to be clear about that.  Water supply improvements would occur when they are not in conflict with fisheries conservation as well as environmental protection, broadly speaking.”

The new biological opinions are driven by science which is absolutely critical, Mr. Souza said.  The old opinions are ten years old, and there have been significant science investments, including many by Metropolitan, that have helped to better understand fisheries conservation and develop broader management strategies that make sense.

It’s important to understand the nature of an Endangered Species Act consultation,” he explained.  “It’s not like we get some proposal from a federal agency like Reclamation and it’s a done deal.  It’s truly a consultation.  There have been significant improvements that were negotiated to the Bureau of Reclamation’s proposed action since it was first released in January.  We had several ensuing months where we worked together on consultation through lots of different challenges.  We had benchmarks for independent peer review under the Water Infrastructure Improvements for the Nation Act (WIIN Act) of 2016.  We were also required to give draft documents to public water agencies like Metropolitan, as well as the state of California, so we worked through all of those questions leading up into the summer months.”

We decided we wanted to have a second independent peer review,” he continued.  “We know how much scrutiny these documents will receive and we thought that was in the public interest to take it to that next level.  We gave the state of California that second draft as well as public water agencies, so we went through two detailed comment periods and did our best to address them in full.”


He then described some of the key provisions of the biological opinions.

Cold water management

Winter-run chinook salmon are imperiled and cold water is necessary to help support spawning.  Mr. Souza said they worked with Reclamation to ensure that there will be cold water to benefit winter-run chinook.  Reclamation has agreed to hold Lake Shasta higher on average on May 1st than they did in the last ten years.

All of the modeling is clear; we will have more cold water to be used in a very targeted way to benefit salmon spawning winter run chinook,” he said.  “The technical framework has a series of tiers that Reclamation uses to identify different kinds of water years, and the modeling clearly shows we’re going to have more tier one and tier two years which is better for fish and fewer tier three and tier four years which are not optimal for fish, and that’s a function essentially of having more cold water to use.

Reclamation, the National Marine Fisheries Service, and the California Department of Fish and Wildlife have agreed to sit down in the spring leading up to the cold water management year and identify a plan that will meter out that cold water in a way to maximize benefits.  They will use performance metrics such as egg to fry survival and temperature mortality to gauge success.

We’re holding ourselves accountable,” he said.  “At the end of every cold management season, Reclamation agreed to do an after-the-fact report to allow us all to take a pause and figure out how we did.  If we see impacts that are outside of the scope that we anticipated, Reclamation agreed to do an independent peer review, so we would unpack that data, find out what happened, and figure out a way to do it better.”

Real-time management of Delta smelt

Mr. Souza acknowledged that Delta operations have long been controversial.  In years past, there have been concerns about entrainment and salvage of Delta smelt, so they have worked with Reclamation and the Department of Water Resources to try and come up with a smarter strategy.  The old biological opinion focused on calendar specific dates for pumping reductions, which meant the date triggered the reductions in pumping, regardless of where the fish happened to be.

Because we have so much better science today, we wanted to see if we could move to real time management so we could be protective of fish and also take advantage of water supply improvements if in fact, those two factors are compatible,” he said.  “We have an investment through the Bureau of Reclamation in a program called Enhanced Delta Smelt Monitoring which we did not have ten years ago.  We have boats out on the water several days a week and we have a much better understanding of the geographic distribution of Delta smelt throughout the San Francisco Bay Delta and we know when they are in the high risk identity areas.”

It’s not just the pumps; there are other factors at play, he said.  In addition to the independent peer review of cold water management, Reclamation also agreed to do a full independent scientific review of the entire Central Valley Project and State Water Project operations at year four and year eight, or twice during the ten year period of the water management plan.

Our goal is clear,” he said.  “We want to be as or more protective than ever.  And we have worked hard to that end.”

Expand salmon distribution

Salmon are imperiled, so the agencies want to expand the geographic distribution of salmon.  So a couple of years ago, the US Fish and Wildlife Service, along with the State of California and the Bureau of Reclamation, began the reintroduction of salmon into Battle Creek, a tributary of the Sacramento River.  The salmon used for the project came from the Livingston Stone and Coleman hatcheries.

I’m happy to say the results are already promising,” Mr. Souza said.  “We’ve seen salmon return this past year and we’re expecting a lot more to come next year.  Year 3 is the return year where we’re expecting to see bigger numbers.  Reclamation has agreed to a $14 million investment over the next ten years so we can continue that restoration effort and hopefully secure the geographic distribution on Battle Creek for salmon.”

Conservation hatchery for Delta smelt

Delta smelt are exceedingly rare and difficult to find, so Mr. Souza said they believe it’s time to be more aggressive with captive propagation of Delta smelt.  Currently, they are capable of producing tens of thousands of fish per year, but he said they want to get that up to hundreds of thousands of fish.  So the environmental documents have been completed and a Record of Decision recently signed for a conservation hatchery for Delta smelt to be constructed in Rio Vista that would allow a significant increase in captive propagation.

Two years ago, a panel of scientists was convened to begin the conversation about captive propagation.  “There had been a lot of resistance leading up to that point, but now it’s almost universally believed in the scientific community that we need to increase captive propagation,” he said.  “This is a tired and true strategy that we used for salmon for generations.  It’s time to that for Delta smelt.  All said and done, this ten year investment is about $1.5 billion for conservation and science.”


Mr. Souza then went into detail about exactly what real time management means.  How can we be smarter and move from the rigid calendar based reductions in pumping?  It’s because of the science investments such as the Enhanced Delta Smelt Monitoring program which has boats on the water several days a week.  It’s also the Metropolitan science investments that have helped to really understand the turbidity issue.  Delta smelt follow turbid water and it’s thought to be a cloaking device as it helps them avoid predators.

So when we see turbid water around the pumps, there’s a potential cause for concern,” he said.  “Reclamation agreed to reduce pumping until that concern is passed.”

For the cold water management plan, they will be monitoring egg to fry survival and temperature management in real-time.  They will be making new investments in steelhead monitoring, because even after all the science investments, they still can’t say what the population estimated size of steelhead is.  He said they are hopeful in a few years that they will be able to give a better answer.

Other things they are doing include visual surveys for redds, carcass surveys to understand the health of the population, and daily juvenile abundance and timing monitoring at Red Bluff.  They will be doing beach seines, Enhanced Delta Smelt Monitoring trawls, and acoustic tagging to understand how fish are distributed through the Delta.  They are also doing genetic testing of the salvage of listed Chinook salmon species versus non-listed Chinook salmon species.


Lastly, Mr. Souza addressed agency relations.  “I want to emphasize our critical partnership with the state of California and public water agencies,” he said.  “We have two projects: the Central Valley Project and the State Water Project; these projects work together.  We know that in the coming days and weeks, the state of California is going to embark on a public review process for its environmental impact review, and my counterpart, Chuck Bonham with the California Department of Fish and Wildlife, will embark upon a permitting process under the California Endangered Species Act.  We stand ready to help assist those efforts.  Whatever we can do to be helpful, we will.  This water is precious, and we all know these projects work their best when they work together.

I also want to acknowledge the leadership around Voluntary Settlement Agreements,” he continued.  “We are very hopeful that these efforts can bear fruit.  If so, we could find ourselves with another significant conservation investment so it would be a wonderful day for California’s environment if those voluntary settlement agreements can get done.”

These are challenging issues and we know how precious the water is in the state of California.  We’re sincere in our desire to meet multiple objectives and recover the species we’re entrusted with protecting.”


One of the directors asked how long Delta smelt are kept in the hatchery before they are released.

Delta smelt live one year, so not too long,” Mr. Souza said.  “We started a couple of scientific experiments already.  What we do is we put them in net pens; we put net pens near Rio Vista which is where the conservation hatchery has been proposed and we also put some in the Deep Water Ship Channel.  The whole purpose was to see how the fish do in the wild.  It’s one thing to grow fish in captivity; it’s another thing all together to put it into real world conditions and deal with it.  The good news is the returns so far have been promising.  We had what we call successful survival; 90% of the Delta smelt we put in the net pen in Rio Vista survived.  So we need to accelerate this work.  We need to move hundreds of thousands into experimental locations.”

You might have heard of some the work they’re doing to try and create fish food, so we have a couple of experiments that have been done over the past couple of years to have a pulse of water go through Yolo Bypass into the Bay Delta.  What we want to do is place Delta smelt in places where we have these food enhancement activities to see if we can get a biological response.”

Another director asked if there have been any concerted studies that have considered projected sea level rise impacts on the smelt and other fish populations.

Yes, and one of the points that I’ll make about climate change has to do with water temperature,” said Mr. Souza.  “There is a relationship with the sea level rise, but there is a growing concern about water temperature increases and what that bodes for the future of Delta smelt.  Two years ago, we had a historically strong water year, and we started to see spawning in the springtime, an uptick, which we found promising.  We were hopeful that was going to translate into a population increase.  This was something we found out because of the Enhanced Delta Smelt Monitoring effort.  We were measuring where the fish were found and what the spawning was looking like, but we saw a population crash of Delta smelt around late June, and the leading hypothesis is that even by California standards, we had a hot and dry summer.  That year, we think water temperature exceeded a lethal threshold, so if you extrapolate that to our climate change future, clearly there is cause for concern.  Delta smelt are not alone in this regard.  I mention salmon need cold water for management and when climate change continues to accelerate and increases water temperature, it will be a concern for many different fisheries.”

What about the nutrient loading from the decay of the levees themselves?

I’m not aware of any studies that have tried to articulate the nutrient loading from levee diminishment, but clearly nutrients have an impact on any water system,” said Mr. Souza.  “We can have algal blooms that take oxygen out of the water and threaten fisheries and essentially they suffocate, so nutrient loading is a concern.  We see it in basins throughout the world that use nutrients to fertilize agriculture; that’s why the habitat restoration component of the proposed action is so critical.  That’s why the voluntary settlement agreements could be such a wonderful advance, because we could see hundreds of millions of dollars become available for habitat restoration.  Wetlands by nature can filter out nutrients from the water column.  It’s a critical component of any healthy environment.


During the Bay Delta Report, Assistant General Manager Roger Patterson noted that the biological opinions are the federal permits for operation of both the CVP and the SWP, but there is also a state permit that must be obtained for the SWP under state CESA.  A draft EIR is expected to be out soon, and after that, there will be an application from DWR to DFW for that permit, so they are expected to start work on issuing that permit early next year.

Mr. Patterson also noted that the October deadline for the voluntary agreements has been pushed off now into December.  They are still working to add more detail into the plan regarding science, governance, water, and habitat, so the goal is mid-December goal to present the plan to the State Water Board.


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