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California Is Giving Water Back to Native Fish – but How Much?

The state proposes to amend hundreds of water rights to help endangered salmon in the San Joaquin River, as well as other species. But there’s lots of disagreement about how much water the fish need to thrive.

Written by Matt Weiser Published on Read time Approx. 8 minutes
These juvenile spring-run Chinook salmon were reintroduced to the San Joaquin River in February 2015 in hopes of re-establishing a self-sustaining population. The State Water Resources Control Board is proposing to amend water rights in the river to boost water flows for the benefit of salmon and other species.Photo by John Walker, Fresno Bee

As California continues an epic regulatory effort to reallocate water supplies for salmon habitat, an equally big question looms over the process: How much water do salmon and other native fish really need?

The question is at the core of a process led by the State Water Resources Control Board to take water from existing human uses – both agriculture and urban – and rededicate it to instream environmental flows in the San Joaquin River, the state’s second-largest river.

The board released a draft proposal in September 2016 that calls for returning the San Joaquin River to 40 percent of its “unimpaired flow.” This means the amount of water that would naturally flow through the river without existing dams and diversions.

Ultimately, the process requires amending hundreds of water rights, a long and hugely controversial undertaking. A similar process will follow on the Sacramento River, the state’s largest.

Is 40 percent of unimpaired flow the right amount of water to revive the San Joaquin and its fish? The answer is vital to the process: If fish don’t get enough water out of the deal, salmon and other species will remain in jeopardy and stiffer regulations will be required.

“All of these government agencies as well as NGOs have studied this question: How much flow do the fish need?” said Jon Rosenfield, a conservation biologist at the Bay Institute, an environmental group that is deeply involved in the process. “We have a breather now to work this out. But we can’t go through another drought like the one we just went through and throw the fish and the environment under the bus.”

Salmon species have received a lot of attention in the process, including endangered spring-run Chinook salmon, which once numbered in the tens of thousands on the San Joaquin River. Fall-run Chinook are also important. While not endangered, they support a lucrative commercial and recreational fishery not only in California, but throughout the Pacific coast.

But the water board’s process is not just about salmon. It’s about improving water quality for a wide variety of species and for overall ecosystem health. More streamflow would also produce better water quality for many urban and agricultural water agencies that divert water downstream.

Yet salmon have become the metric by which other benefits are calculated, because restoring salmon populations is not only a legal mandate but also one of the trickiest problems to fix. And there is ample evidence that boosting runoff to 40 percent of unimpaired flow is not enough.

The California Department of Fish and Wildlife reported in 2013 – in lengthy comments to the state water board – that much more flow may be necessary.

“Substantial evidence demonstrates that approximately 50 to 60 percent unimpaired flow is the minimum necessary to reestablish and sustain fish and wildlife beneficial uses,” the agency wrote.

The National Marine Fisheries Service, the federal agency charged with protecting salmon, wrote in a 2009 biological opinion that 40 percent might not be enough to protect salmon in the Stanislaus River, one of the San Joaquin tributaries that is the focus of the state water board’s currently regulatory effort. Flows above 40 percent, the agency wrote, are necessary “to avoid the limited biological purpose of avoiding species jeopardy.”

The state water board itself acknowledged that 40 percent is a compromise. Its own “flow criteria” report in 2010 concluded that the target in the San Joaquin River should be 60 percent of unimpaired flow.

Les Grober, the water board’s deputy director for water rights, said the 40 percent target is meant to accommodate other critical water uses that depend on the river, such as cities and farms. The proposal actually allows a range of flows from 30 to 50 percent, he said. Depending on conditions, an expert panel could adjust the flow requirement on a near real-time basis.

For instance, if monitoring indicated fish might need extra flow in the fall, the unimpaired flow target could be reduced in the springtime to conserve water for later in the year. This could also help farmers plan their own water demand and planting decisions.

“Our process takes into account the best available science and also looks at policy implications,” Grober said. “This is saying, since there are so many other users of water, you can’t provide for all the fish and wildlife functions, so here’s a budget for doing the best you can.”

The water board has received thousands of public comments on its 40 percent flow proposal. It expects a final proposal and a formal response to all those comments sometime this fall.

The board has the legal authority to take back water rights when public trust resources, such as Chinook salmon populations, are threatened. But it has rarely exercised that authority, partly because to do so requires long and painful deliberations that are likely to result in litigation.

The board’s process is effectively a water-quality action: It is proclaiming that streamflows aren’t sufficient to keep water temperatures cold enough for salmon survival.

The federal Clean Water Act requires the water board to review streamflows every three years to maintain healthy water quality. In the case of the San Joaquin River, the board is more than 20 years late: Streamflows have not been comprehensively updated since 1995. As part of the water-quality plan it adopted that year, the water board also set a goal to double salmon populations, a target that has never been achieved.

The San Joaquin River, shown here, has been heavily impacted by water diversions, upstream dams and habitat loss. It once hosted several salmon runs numbering in the tens of thousands, but some have been eliminated entirely and others reduced to just a few hundred fish. (Photo Courtesy U.S. Fish and Wildlife Service)

Rosenfield said the 40 percent goal is not enough to achieve the salmon-doubling goal. That’s partly because flows also influence water temperatures and habitat availability in the river. Fish – and salmon especially – are sensitive to temperature.

The San Joaquin in particular is a long river, exposed to a lot of heat and sunlight as it moves downstream. More flow helps keep water temperatures cool enough so that salmon and other fish can thrive. Greater flow also opens up side channels that protect fish from predators and provide resting areas.

“The more water you add to the river, the more habitat you get,” Rosenfield said. “And 40 percent doesn’t get there. It doesn’t inundate the right amount of rearing habitat to support the populations you need. To be fair, 50 percent and 60 percent don’t get you there either. But they get more habitat.”

Water agencies affected by the process want even less flow. They are reluctant to throw out hard numbers. But almost universally, they oppose the 40 percent goal.

One is the San Francisco Public Utility Commission (SFPUC), which diverts water from the Tuolumne River, one of the San Joaquin tributaries targeted by the water board for flow changes. The district serves not only San Francisco residents but also sells wholesale water to several other Bay Area utilities.

Steve Ritchie, assistant general manager for water at SFPUC, called the water board’s process to amend streamflows “a meat cleaver-like approach.”

He said, “Historically, people have wanted to turn the flow knob because it’s the easiest knob to turn,” adding, “and if it doesn’t work, well, then they ask for more flow. But we think we can do better things on the Tuolumne River.”

He acknowledges SFPUC will have to give up “some water” to improve aquatic habitat. But the agency also proposes other actions that it believes will take the place of higher flows, such as restoring spawning gravel habitat in the river and planting more riparian trees on riverbanks to cast shade that will reduce water temperatures.

The Modesto Irrigation District also favors this approach. Among other things, it proposes an aggressive program to control invasive predator fish, such as striped bass, which devour native species.

“There are a lot of nonflow measures that will have a greater impact than flow,” said Jake Wenger, vice president of the district’s board of directors. “We’re putting up real projects with real money. At the same time, we are offering water.”

Settlement talks between water agencies and environmental groups have been underway for months. The process, led by former interior secretary Bruce Babbitt, aims to find a compromise package of streamflow and habitat restoration that will please everyone.

All the parties hope a settlement can be reached, because it would bring relief to fish species a lot sooner, avoiding a cumbersome years-long process at the water board to amend hundreds of water rights.

A white sturgeon being examined on the banks of the San Joaquin River. Efforts by the State Water Resources Control Board to improve flows in the river would benefit a wide variety of species, including those not yet considered endangered, including the white sturgeon. (Photo courtesy U.S. Fish and Wildlife Service)

The water board also hopes a settlement can be reached, partly because it would ensure habitat restoration activities are part of the solution. The board does not have the legal authority to require water users to undertake habitat restoration projects.

“The bottom line is, there cannot be one [flow] number because this isn’t just about fully protecting the one use in all situations,” Grober said. “This is all about coming up with something that would reasonably protect the one [wildlife] use and doesn’t have an unreasonably large effect on other uses.”

Peter Moyle, an emeritus professor of fisheries biology at the University of California, Davis, agreed that there may not be a magic flow number. A smaller flow increase could make a big difference if accompanied by aggressive habitat restoration. But he said the flows must be carefully managed so they occur when fish need water most.

“The more water the better. There’s no question about it,” said Moyle, who has spent a lifetime studying the rivers and fish in question. “But I’m also recognizing there’s huge competition for water, and if we don’t make some compromises, then changes in the political winds could really result in something much worse than we have today.”

He points out the primary goal is not just to revive salmon populations, but to bring back a “living river.” A compromise involving less streamflow could still be transformative for many other species, he said, even if it’s not ideal for salmon.

He cites the riparian brush rabbit as an example of another “charismatic” species that could benefit from more streamflow. The tiny rabbit, an endangered species, depends on floodplains and dense riverside vegetation for its food and shelter. And without more streamflow, there will never be enough of those habitats to restore the rabbit population.

“It kind of bothers me, actually, that the focus is so much on salmon,” Moyle said. “There are so many benefits to other species out there, including other endangered species. I just would like to avoid contention on a lot of these issues, because there are so many good things that come out of having a living river.”

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