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As Californians Fight Over Fresh Water, the San Francisco Bay Barely Survives

Drought, industrial-scale agriculture, and an outdated water rights system are killing the largest estuary in the American West, according to a new report. In the coming year, the state’s residents have a rare opportunity to turn things around.

By Jimmy Tobias


San Francisco, Oakland, and the Bay Bridge, 2014. (Photo: Wikimedia Commons)

The San Francisco Bay is an estuary — an ecological mixing bowl where salty waters from the Pacific Ocean meet the fresh runoff that flows down from the high sierra through the Sacramento and San Joaquin rivers and eventually to the sea. The brackish blending together of these aquatic inputs produces one of the most abundant ecosystems on the planet. Shrimp, crabs, smelt, salmon, and many small but supremely important invertebrates swim (or scuttle) in its mild waters. Cormorants, pelicans, geese, and ducks galore wing overhead or waddle along its shores. Mammals, including whales, seals, and some humans too, depend on its productivity for their very survival. It is the beating heart of its urban namesake, that West Coast capital we call the Bay Area.

But the Bay is in a very bad way. According to a major recent report, thousands of dams and ditches that supply irrigation and drinking water to industrial farms and dense cities throughout California now deprive the estuary of as much as 70 percent of its freshwater inflow during the crucial winter and spring months each year. Even before the present debilitating dry spell, it had experienced its own man-made drought for decades. The largest estuary in the American West is being starved of fresh water, while its life-supporting brackish zone shrinks in the face of increasing salinity. The complex relationships that keep the ecosystem intact are fraying every day.

Jonathan Rosenfield is a conservation biologist with the Bay Institute and the lead author of the report “The San Francisco Bay: The Freshwater-Starved Estuary.” Commissioned by the quasi-governmental San Francisco Estuary Partnership, it is a meticulous description of disaster: The report speaks of sharp declines of shrimp and salmon populations. It speaks of dangerous algae blooms and degraded water quality. It speaks of sediment deprivation and beach erosion. It speaks of commercial fishery closures and the loss of thousands of jobs in recent decades. It speaks of a brewing catastrophe for migratory birds and beloved marine mammals.

“Looking at all the signs,” Rosenfield says, “it is clear the ecosystem will collapse.”

This year, however, Californians have a chance — a rare and controversial opportunity — to clean up their act.

The foremost reason for the San Francisco Bay’s woes, according to the report, is large-scale farming that relies on an antiquated and over-allocated water rights system. In fact agricultural irrigation, a traditionally water-intensive form of land use, accounts for approximately 80 percent of the fresh water diverted from the Bay watershed each year. Drinking water provision for cities like Sacramento, San Francisco, Merced, and Modesto makes up much of the rest.

Agriculture’s excessive share of the Bay’s fresh water, however, may soon be subject to a shrinking. The California State Water Resources Control Board — a government agency that enforces clean water standards and oversees the allocation of the state’s scarce life-giving liquid — is in the midst of revising regulations that control how much water is removed from the Sacramento and San Joaquin watersheds. These rivers and their tributaries are the principle source of the Bay’s fresh water supply. This sort of regulation rewrite is rare — the last meaningful update took place in 1996.

“The water quality control plan update is the biggest thing in California water policy that will happen in our generation,” says Rosenfield, whose team published its report in part to inform this bid for regulatory reform.

“To try to return a major portion of these rivers to in-stream uses after developing an economy and a lifestyle and a livelihood for so many people will be bad for just about everybody but the fish.”

In September, the State Water Resources Control Board, or the Board, put forward a draft proposal that could keep intact 40 percent of the San Joaquin watershed’s natural flow during the crucial winter and spring months. (As it now stands, as much as 90 percent of the water from the San Joaquin and its tributaries is requisitioned by human users during the wet season.) And though it has not yet put out any proposals for the Sacramento River, the Board has released a scientific report that suggests the possibility of leaving as much as 75 percent of that river system’s natural flow untouched during the same winter-spring timeframe.

Such reforms are essential if the decrepit estuary and its withering fish populations are to heal. But the response to these ideas has been “polarized,” Rosenfield says. Some people, he says, “think the sky is falling.”

Agricultural interests, for instance, have already denounced the San Joaquin draft proposal as well as the Sacramento scientific report.

“To try to return a major portion of these rivers to in-stream uses after developing an economy and a lifestyle and a livelihood for so many people will be bad for just about everybody but the fish,” says Chris Scheuring, a farmer and lawyer for the California Farm Bureau Federation. The federation’s members fear that restrictive flow plans will force the idling of more than 200,000 working acres across the state.

Agriculture is not alone of course. The city of San Francisco also sees the Board’s draft policy as a threat. In an October op-ed in the San Francisco Chronicle, Bay Area water officials fretted over the idea of leaving 40 percent of the San Joaquin’s winter and spring flow unused. The city, after all, gets its drinking water supply from one of the river’s large tributaries.

“With the proposal,” they wrote, “we can expect more severe and more frequent water rationing.”

Water advocates, conservationists, and commercial fishermen, meanwhile, support the Board’s overall goals, though some say its recent proposal doesn’t go far enough.

“People would still be able to divert between 50 and 70 percent of [the San Joaquin system’s] flow,” says Doug Obegi, a senior attorney with the Natural Resources Defense Council. “That is substantially more diversion than what the California Department of Fish and Wildlife and other agencies have recommended as necessary to restore the health of these rivers.”

Jonathan Rosenfield agrees. “When we look at the [Board’s] proposal, it is very clear that it is not what science from agencies, independent experts, and the board itself has indicated will be necessary to restore populations of salmon as the law requires,” he says.

As this once-in-a-generation struggle to change California water allocation continues in the coming years, it’s wise to remember the debate’s broader context. Like one tale in a larger tome, the San Francisco estuary’s unraveling is embedded in more comprehensive crises.

In California, freshwater ecosystems as a whole are in a state of severe distress due to burgeoning human populations as well as carbon pollution. A 2015 study published in PLoS One describes the problem precisely:

Water allocations are currently five times the state’s mean annual runoff and, in many of the state’s major river basin, rights to divert water lay claim to up to 1,000% of natural surface water supplies. Recent studies have highlighted dramatic declines of California native fishes with 80% either extinct or threatened with extinction within 100 years.

As things stand today, most of the state’s fish, including many in its biggest estuary, have no future.

And the Golden State is just one front in the quiet quotidian war on wildlife and wild systems. As the Guardianrecently reported, a new study by the Living Planet Index found that the number of wild animals on planet Earth is on track to decline as much as two-thirds by 2020. The major industries driving this ineffable loss include logging and, you guessed it, agriculture.

If you want to catch a first-hand glimpse of this galling global catastrophe, the Bay is Exhibit A.