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Delta smelt monitors work near Rio Vista. The collapse of the estuary has driven the 3-inch fish to the brink of extinction. (US Fish and Wildlife Service photo)
Delta smelt monitors work near Rio Vista. The collapse of the estuary has driven the 3-inch fish to the brink of extinction. (US Fish and Wildlife Service photo)
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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.”

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.

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.

‘Not sustainable’

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.

Fishery devastation

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.

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.”

CALmatters.org is a nonprofit news venture covering state policy and politics.