Western Water Excerpt Gary Pitzer Jennifer Bowles

Preservation and Restoration: Salmon in Northern California
Winter 2017

Protecting and restoring California’s populations of threatened and endangered Chinook salmon and steelhead trout have been a big part of the state’s water management picture for more than 20 years. Significant resources have been dedicated to helping the various runs of the iconic fish, with successes and setbacks. In a landscape dramatically altered from its natural setting, finding a balance between the competing demands for water is challenging.

Read the excerpt below from the Winter 2017 issue written by Gary Pitzer along with the editor’s note from Jennifer Bowles. Click here to subscribe to Western Water, a quarterly magazine, or to purchase just this issue.


Protecting and restoring California’s populations of threatened and endangered Chinook salmon and steelhead trout have been a big part of the state’s water management picture for more than 20 years. Significant resources have been dedicated to helping the various runs of the iconic fish, with successes and setbacks. In a landscape dramatically altered from its natural setting, finding a balance between the competing demands for water is challenging.

Millions of wild salmon once returned to spawn in the foothills and mountains of the Central Valley, nurtured by countless streams and tributaries full of cold water running from the Sierra Nevada and southern Cascade mountains.

As California’s population grew, dramatic changes to the landscape caused a steep decline in the abundance, distribution and diversity of these fish. Gold mining, logging, dam construction, water and hydropower management and other land uses severely impacted fish populations.

Ultimately, Sacramento River winter-run Chinook salmon were listed under the federal Endangered Species Act (ESA) as endangered in 1994, Central Valley spring-run Chinook salmon were listed as threatened in 1999, and California Central Valley steelhead were listed as threatened in 2006. Finding the means to help salmon survive is controversial. Regulating flows to facilitate spawning and migration sometimes means withholding water to farmers and urban dwellers that depend on timely deliveries.

Balancing water deliveries with environmental needs is a complicated process fraught with peril. In 2009, the Delta Reform Act required the State Water Resources Control Board (State Water Board) to come up with appropriate flow criteria for the Sacramento-San Joaquin Delta (Delta). In their 2010 report, State Water Board staff noted the complexity of the matter:

“While folks ask ‘How much water do fish need?’ they might well also ask, ‘How much habitat of different types and locations, suitable water quality, improved food supply and fewer invasive species that is maintained by better governance institutions, competent implementation and directed research do fish need?’” the report said. “We cannot know all of this now, perhaps ever, but we do know things that should help us move in a better direction, especially the urgency for being proactive. We do know that current policies have been disastrous for desirable fish. It took over a century to change the Delta’s ecosystem to a less desirable state; it will take many decades to put it back together again with a different physical, biological, economic, and institutional environment.”

Scientists are busy on several fronts in an effort to better understand all life stages of the species so that better tools can be developed to ensure their survival. Spearheading the effort is the National Marine Fisheries Service (NMFS), which in 2016 included the winter-run Chinook salmon as one of eight “Species in the Spotlight” among the most at risk for extinction in the near future. “The ongoing drought has intensified California’s water management challenges and accentuated the urgent and critical need to reintroduce winter-run Chinook salmon populations into their historical habitat [in the upper Sacramento Valley], an area which is not dependent on Shasta Reservoir storage and is somewhat buffered from drought by the influence of cold water springs,” NMFS’ 2016 Winter-run Chinook Salmon Five-Year Action Plan says. (NMFS also is known as NOAA Fisheries. The National Oceanic and Atmospheric Administration is an agency within the Department of Commerce.)

According to the 16-page publication, “the survival and recovery of winter-run Chinook salmon cannot be achieved without establishing additional populations.”

Measuring the relative health of the state’s various runs of Chinook salmon is a year-to-year endeavor, with many factors influencing the number of returning fish. Along their entire range, Chinook salmon complete their life cycle in two to eight years, but the vast majority of Central Valley Chinook complete their life cycle in two to four years, with three years being the most frequent.

The spawning Chinook adults of 2016 were born in 2013 during the depths of the drought, meaning there were fewer of them to begin with because of egg mortality. Biologists also said poor ocean conditions last year mean the salmon returning to the rivers and creeks in the upper Sacramento Valley are smaller, which in turn reduces the number of eggs each female lays.

While drought is nothing new to California, the dry period commencing in 2012 has been especially hard on salmon, pushing the abilities of federal and state agencies to deal with the crisis. Record-low river levels meant hatchery-raised smolts had to be carried in trucks downstream in 2014 and 2015.

“The last three years have really been more intense and long-term than earlier periods,” said Josh Israel, biologist with the Bureau of Reclamation (Reclamation) at the 2016 Bay-Delta Science Conference in Sacramento. “Many people think we are on the verge of a mass extinction event. Hopefully, we can understand it before it’s too late.”

Multiple restoration projects have been completed or are ongoing in the northern Sacramento Valley along the namesake river and its creeks to help salmon, aided by state and federal agencies and local water users. On the San Joaquin River south of Sacramento, it remains to be seen whether a population of spring-run Chinook can be re-introduced into a system so changed by water diversion and flood control projects.

The San Joaquin River Restoration Program being implemented by Reclamation and other federal and state agencies aims to re-establish one of the most vibrant populations of spring-run Chinook on the West Coast. Draining the southern portion of the Central Valley, the San Joaquin River originates in the highest peaks of the Sierra Nevada and flows toward the Delta. The program includes habitat restoration, river reconfiguration and hatchery facilitation. After more than 70 years since its extirpation, progress in reviving the salmon run has been a challenge.

“Early on in the program, the hope was to have a connected river with all the necessary improvement projects done by 2014,” said Jeff Abrams, fisheries biologist with NMFS’ San Joaquin River Basin Branch. “Although progress has been made, that hasn’t happened as we have discovered that restoring the river is a more involved process than initially anticipated.”

Scientists are doing a variety of things to better understand how to preserve, protect and restore what were once-thriving salmon populations in Northern and Central California.

“We are trying to look at the entire life cycle, not just one thing or another,” Maria Rea, assistant regional administrator with NOAA Fisheries, said at the science conference.

The most vulnerable fish is the winter-run Chinook, which have been hammered by more than five years of drought and other factors that have driven their numbers to near extinction.

“Without marshalling our resources and heightening our engagement with vital partners, Sacramento River winter-run Chinook salmon may be lost to future generations,” NMFS’ Action Plan said in reference to the long drought.

Adult winter-run Chinook salmon migrate from the ocean to Sacramento River spawning areas from December through July. The winter-run is one of four runs found in the river. The winter-run stand apart from fall-run because although they come up river in the winter, they stay in fresh water for a longer period of time – not spawning until summer. The fall-run spawn within weeks of migrating from the ocean to the fresh water. Spawning for winter-run has to occur in cold water (56 degrees Fahrenheit) and takes place from late-April to mid-August.

Despite efforts to maintain that temperature, officials haven’t been able to meet that standard – especially during the recent drought. “Things started getting really bad in 2014,” said Eric Danner, research ecologist with NMFS, speaking at the science conference. “We ran out of cold water half way through.”

Salmon are anadromous fish. They are born in fresh water, spend most of their lives in the sea and return to fresh water to spawn, usually to the same waterway in which they were hatched. Thus they are vulnerable to ecological challenges in the ocean and the state’s streams and rivers.

In its update of the Bay-Delta Water Quality Control Plan, the State Water Board is calling for increased instream flows for the Sacramento and San Joaquin rivers and their tributaries to protect fish, which means less water for rights holders.

“The odds of [salmon] survival are decreasing and will continue to decrease unless action is taken,” State Water Board Chair Felicia Marcus wrote after a new draft of the first phase of the plan update was released in September 2016.

The rate of diversion on the Stanislaus, Tuolumne and Merced rivers, “at critical times of the year, well over 60 percent – and in some cases and times more than 80 percent,” is not sustainable, Marcus wrote, noting that salmon and steelhead “are in serious decline.”

In response, a coalition of more than two dozen government and water user organizations in Stanislaus and Merced counties lashed out at the plan, calling it a “water grab … without mitigation or due analysis of impacts.”

There is concern from Sacramento River water rights holders as well.

“We don’t think we have the luxury in the state of California with 39 million people to do mass evacuations of water storage without a real specific purpose in mind,” David Guy, executive director of the Northern California Water Association (NCWA) told the State Water Board at a Dec. 7 public hearing on the science used for the updated water quality plan. “We’ve got to find a better approach that works for 2016 and looking forward.”

Guy said he’s concerned the updated water quality plan could disrupt many of the existing standards painstakingly enacted through the years.

“Importantly, all of these flow agreements were finalized and executed since the last update of the Bay-Delta Water Quality Control Plan,” he said. “Let’s be careful about unwinding some of these agreements, some of which took 30 years and a couple trips to the Supreme Court.”

Editor’s Note: Wave of change

When a new federal administration takes over in Washington, D.C. – whether it’s Democratic or Republican and whether or not it’s the same political party in power – questions always abound about what direction policy will take on the federal stage.

In the water world in California, there are several big questions – how will the administration support infrastructure projects, notably the controversial twin tunnels below the Delta known as the WaterFix. And what about the Salton Sea, once championed by the late entertainer-turned-Congressman Sonny Bono and now awaiting an unknown fate at the end of this year.

There are also big questions along the Colorado River, where the rush to get a series of agreements signed before then-President Obama left office never materialized. Two days before Donald Trump’s presidential inauguration, Interior Secretary Sally Jewel issued a memo outlining a game plan for avoiding water shortages along the Colorado and underscoring the importance of concluding a drought contingency plan among California, Arizona and Nevada as well as a cooperative agreement known as Minute 32X between the U.S. and Mexico governments to share in reduced water deliveries to prevent reservoirs from falling to critical lows.

So will Trump follow through? Could his positions on immigration and building a wall along the Mexican border play a role?

We will attempt to answer these questions about the Colorado River at our flagship conference of the year, the Executive Briefing, on March 23 in Sacramento, with a panel made up of Lower Basin representatives.

And will the Endangered Species Act, what some consider the nation’s most powerful environmental law be at risk? In the water world, it not only protects the listed fish that ply the rivers, but those listed plants, birds and even kangaroo rats that live on their banks or flood plain. This issue of Western Water magazine explores what’s being done to help endangered salmon, and the different runs that migrate between the ocean and the Sacramento and San Joaquin systems.

The Endangered Species Act was signed into law in 1973 by a Republican president (Richard Nixon), mainly in reaction to the demise of the bald eagle. However the first test of the Act in court was water-related; it involved a tiny fish in Tennessee known as the snail darter and the construction of a dam. Interesting times are indeed ahead. Hope to see you at our Executive Briefing.

Referring Pages