The depleted Sacramento-San Joaquin Delta is suffering from water diversion to farms and cities.

The depleted Sacramento-San Joaquin Delta is suffering from water diversion to farms and cities. (Mark Andrew Boyer/KQED)

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The report’s findings were unequivocal: Given the current pace of water diversions, the San Francisco Bay and the Delta network of rivers and marshes are ecological goners, with many of its native fish species now experiencing a “sixth extinction,” environmental science’s most-dire definition of ecosystem collapse.

Once a vast, soaked marsh and channel fed by the gushing Sacramento and San Joaquin rivers, the Delta has diminished dramatically over the previous century as those rivers and their mountain tributaries have been diverted to irrigate Central Valley farms and Bay Area urbanity. With winnowing supplies of Chinook salmon available for food, Orcas off the coast are starving. So, too, are seals and fish-eating birds. And the Gulf of the Farallones, a national marine sanctuary, is suffering from a lack of freshwater fed by the Bay.

Those grim conclusions in this fall’s report by scientists at the Bay Institute, an environmental group focused on the bay’s ecosystem, would normally have set off alarm bells — except that those warnings have been sounding for decades. That’s about as long as state agencies have been in the planning process to re-plumb the region that supplies close to half of California’s water and supports world-leading agricultural production, fisheries and tourism.

The state’s goal: recalibrate the water flows that have drained vital rivers down to as low as 10 percent of their natural levels — just a fifth of the 60 percent flow scientists say is necessary to preserve the ecosystem.

But the mechanism for change — the state water board’s much-anticipated update to its Bay-Delta plan — is running “way, way behind,” according to board officials. The plan hasn’t had a significant update in more than two decades. And recent progress has been agonizingly slow.

The first of the plan’s phases — setting targets for turning the tap on and off on the vanishing San Joaquin river, and for reducing water salinity — has been six years in the making and runs thousands of pages long. It isn’t expected to be finalized until next summer.

After analyzing possible flow rates, the state board’s staff, in its draft, sets a target that would have to be met: an “adaptive range” of 30 to 50 percent of the average unimpeded water flow for the San Joaquin River and its key tributaries, the Merced, Stanislaus and Tuolumne rivers. Such a flow, averaging about 40 percent, will “provide reasonable protection of fish and wildlife while moderating impacts to water supply for drinking water and agriculture.”

Fed by mountain tributaries, the San Joaquin River runs up the spine of California before flowing into Delta.
Fed by mountain tributaries, the San Joaquin River runs up the spine of California before flowing into Delta.

In a later phase, at best a few years down the road, the state will play the role of Solomon, determining which competing parties get what amount of water.

As is the way with California water policy, everyone’s share of water is going to be cut, so no one is happy. Farmers predict fallowing of crops, Bay Area officials say impeding development will drive up housing prices, rural counties say the policies are inhibiting growth, and environmental groups still insist that not enough water is being set aside to maintain the health of the complex water system and the fish and wildlife that depend on it.

And, as the tedious, divisive planning process creeps along, the region’s economy is at a standstill. Farms and harbors are in disrepair, private sector investments have withered, and residents are waiting for a consistent policy from Sacramento. Further adding to the uncertainty is the incipient presidency of Donald Trump, who, while campaigning in Fresno in May, proclaimed that it was “insane” to “shove water out to the sea” on behalf of endangered fish.

Nobody knows quite what to expect from a Trump administration, but it could try to undermine the state effort by withholding federal funds for restoration of the San Joaquin River and by relaxing federal Endangered Species Act protections. A Republican-controlled Congress also could weigh in by passing federal laws governing how water is divvied up.


“We all know that the Delta as it exists today is not sustainable,” said Michael George, who serves as the Delta Watermaster for the state Water Resources Control Board. “People have been waiting for a policy and no one is making any long term investments because the policy is so uncertain. There’s wariness. Nobody in the Delta wants Sacramento to do anything other than go away,”

There’s not enough water to satisfy all takers and that is not likely to change. What will have to change is the way scarce water supplies are allocated.

“It’s a game of musical chairs right now and we are missing about three chairs,” said Chris Scheuring, a water lawyer for the California Farm Bureau Federation, which is fighting to preserve water supplies on behalf of the state’s powerful agriculture industry. “It’s a zero-sum game and somebody has to lose. The drought has intensified. Climate change is on the horizon. We have a declining snow pack. This is putting us on the path of an epic train wreck.”

The situation has come down to powerful forces wrestling over a few drops. At any given time more than 80 percent of the water that would naturally flow through the various rivers, tributaries and sloughs feeding the Delta and Bay is siphoned off for storage, agricultural or municipal use. What comes out the south end, or into the San Francisco Bay, is often less a flow than a trickle. The San Joaquin River, for example, at some points has become almost a dry bed, its key tributaries also tapped (the Tuolumne, for example, feeds the Hetch Hetchy Reservoir that supports San Francisco.) As a result, last year less than 10 percent of the San Joaquin River’s water was available to replenish the Delta.

The catastrophic collapse of the estuary has driven the three-inch Delta Smelt to the brink of extinction and decimated the Sacramento Splittail, as well as two runs of chinook salmon, Central Valley steelhead, among others. The first phase of the state’s plan, by setting its 40 percent flow target, attempts to help fish populations recover.

The tiny, endangered Delta Smelt is vanishing -- a consequence of an over-tapped estuary.
The tiny, endangered Delta Smelt is vanishing — a consequence of an over-tapped estuary.
(U.S. Fish and Wildlife Service)

Although that flow would amount to a veritable flood in sections that are seeing less than 10 percent of natural levels, it would still be one-third below the board’s own 2010 analysis that pegged 60 percent flow as best for fisheries recovery.

“If the 40 standard does anything beneficial for the fish, it sends them to extinction less quickly,” said Jon Rosenfield, the lead scientist on the Bay Institute report. “Chinook salmon are the hardiest fish species we know of. They colonized every watershed from Monterey through Alaska to Japan. If Chinook salmon cannot live in your rivers, something is very, very wrong.”

But water board chairwoman Felicia Marcus stressed that a 60 percent standard represents “what fish would have asked for if the fish could talk” — and that the final plan must balance the needs of all water users.

“I was stunned to see that over half the time we are diverting 80 and as much as 90 percent of water out of these rivers. That’s gonna be tough on these fish,” she said. “At the same time, people have to realize you can’t put it all back. We’re coming to grips with where we’ve been and where we need to go. We need to figure out how to share the rivers and water more thoughtfully, between human use and nature.”

What’s good for the fish is often in conflict with the reality of a region that has been markedly altered by human hands. Nineteenth-century federal policy that favored bending nature to boost commerce meant draining the Delta’s marshes and swamps to make way for farming islands and ever-growing settlement. Today an estimated 98 percent of the Delta’s historic tidal wetlands have disappeared.

“We don’t have enough water to serve all of the demands that we put on it,” George said. It’s not farms versus fish, not cities versus rural areas, not North verses South. It’s an all-of-the-above crisis.

Wildlife on the Farallones -- a marine sanctuary outside San Francisco Bay -- are also suffering due to a lack of freshwater flowing from the Delta.
Wildlife on the Farallones — a marine sanctuary outside San Francisco Bay — are also suffering due to a lack of freshwater flowing from the Delta.

Much of the Delta’s farm-to-town economy is dormant, as investors have waited for consistent signals from Sacramento about the future of water policy. Farm machinery sits rusting and once-busy marinas and docks are choked with mats of invasive water hyacinth.

“The economy is stagnant, uncertainty about policy has been hanging there for a decade,” said Jeffrey Michael, director of the Center for Business and Policy Research at the University of the Pacific in Stockton.

The farm bureau’s Scheuring said growers have adopted new water methods that have enabled them to produce twice the value of crops with the same amount of water as they required 30 years ago. Now, he says, farmers can’t give up any more water.

Neither can San Francisco, according to Charles Sheehan, spokesman for the city’s Public Utilities Commission. The region’s 2.6 million frugal customers are already consuming water at less than half the statewide average, he said. Less water has meant shorter showers, browner public parks and, officials say, restrictive economic development. More restrictions could restrict new development, further driving up home prices.

The crisis also takes a toll on other industries. A federal report showed the value of California’s fishing harvest plummeted 53 percent last year.

Across the state, people are lining up to recount tales of water woes. Often at the top of their lungs. In recent months, Stanislaus County officials flatly accused state water officials of lying — and the rhetoric at a Merced County Board of Supervisors meeting got so overheated that one citizen compared the impact of the Delta plan on farmers to the Holocaust.

“It’s not the most comfortable place to be, people are always mad at you,” said Marcus, the state water board’s chair. “But we are going to make these decisions. Either you help us make the decision or we are going to move.”

CALmatters.org is a nonprofit news venture devoted to coverage of state policy and politics.

  • Richard Solomon

    It is clear that ALL of us in Calif cannot continue to use water as we have in the past. The population has doubled since the 1960’s but our water usage plans have not kept up. The rhetoric has to tone down and constructive give and take has to come from everyone: urban and agriculture, north and south, etc.

    From what I have read, the Twin Delta Tunnels offers more of the same. Do we need to develop alternative plans?

  • Pixie Camembert

    Why no mention of Governor Brown’s tunnels? They will take even more water away from the Delta and would be DISASTEROUS for what’s left of local eco systems.