California Forum

What will it take to make San Joaquin River system healthy again?

The Eastside bypass of the of the San Joaquin River restoration project is shown where water flows in Merced County. A decade ago, environmentalists and the federal government agreed to revive a 150-mile stretch of California’s second-longest river, an ambitious effort aimed at allowing salmon to again swim up to the Sierra Nevada foothills to spawn.
The Eastside bypass of the of the San Joaquin River restoration project is shown where water flows in Merced County. A decade ago, environmentalists and the federal government agreed to revive a 150-mile stretch of California’s second-longest river, an ambitious effort aimed at allowing salmon to again swim up to the Sierra Nevada foothills to spawn. The Associated Press

In 1877, an early explorer of the Yosemite backcountry descended from the mountains and opted to take what was, then, an expedient route back to the Bay Area: He built a raft out of wood and floated home.

He launched his craft on the lower reaches of the Merced River and then entered the San Joaquin River, which carried him all the way through the Sacramento-San Joaquin Delta.

The man was John Muir. He was 39 years old.

“The amount of water in the river – a dry year – is about a current ten feet wide 2 feet deep flowing 3 miles per hour,” Muir wrote in his journal from the trip. “Some fine reaches, glassy slipping current. Salmon in great numbers making their way up the river for the first time this season.”

It was November, often the driest time of year for California rivers, and yet there was enough water for Muir and the salmon to travel home.

Such a trip is almost unimaginable today. The San Joaquin, California’s second-largest river, rarely has any discernible flow. The tributary rivers Muir saw – the Merced, Tuolumne and Stanislaus – are dammed and tapped by hundreds of private water diversions.

Salmon are still found, but they can be counted in the dozens.

It might not always be this way. In a long-overdue process, the State Water Resources Control Board plans to order hundreds of users to leave more water in the San Joaquin River and its tributaries. The result will be improved water quality, colder water and more water – for fish and would-be raft builders.

This may be one of the most contentious government actions California has seen in a generation. The affected diverters – mostly farmers – have enjoyed nearly unlimited access to water for a century or more.

“We recognize that it is very hard to do,” said Les Grober, the water board’s deputy director for water rights. “It just means we all have to be smarter about using this precious resource for maximizing all of these uses.”

The water board proposes returning to the San Joaquin River 40 percent of its “unimpaired flow.” This means the amount of water that would naturally flow through the river without existing dams and diversions.

The 40 percent target also applies to three tributary rivers: the Merced, Tuolumne and Stanislaus. Actual median flow in those tributaries from 1986 to 2004 were 26, 21 and 40 percent of unimpaired flow, respectively.

Returning flows to 40 percent is less than what the science has recommended, and it may not be enough to bring back native fish species from the brink of extinction. Science, in the form of a flow criteria study ordered by the Legislature in 2009, recommended 60 percent.

Forty percent is an act of regulatory compromise. It recognizes California is now heavily dependent on the river for drinking water, crop irrigation and hydropower generation. Getting the river back to 60 percent of its natural flow could be too damaging to all these important uses.

Even wealthy and powerful San Francisco is affected, because its Hetch Hetchy water system diverts about 244,000 acre-feet annually from the Tuolumne River.

“People are going to lose water. I think it’s a very big deal,” said Chris Shutes, a water rights advocate with the California Sportfishing Protection Alliance and a supporter of more river flow. “It’s one of those things people have been putting off for a long time because it involves hard decisions where there’s not enough water to meet everyone’s needs.”

San Francisco officials estimate the proposed cuts to their Tuolumne River diversions could require water rationing of 42 percent or more in severe droughts, which they’ve called “untenable.”

“Under these conditions, it’s hard to see how our communities would continue to thrive and prosper,” Harlan Kelly Jr., general manager of the San Francisco Public Utilities Commission, wrote in an op-ed published Oct. 7 by the San Francisco Chronicle.

In the South San Joaquin Irrigation District, general manager Peter Rietkerk estimates water users on the Stanislaus River may lose 79,000 acre-feet per year on average. That’s about a 13 percent cut to the 600,000 acre-feet of water rights shared by Rietkerk’s district and the Oakdale Irrigation District.

“It would be unheard of for our region,” Rietkerk said. “We would basically have available for our customers (in drought years) about 1 acre-foot of water per acre. That’s less than meaningful for any crop you can grow.”

But it might not be as painful as some think. In just two of the counties directly affected by the water board’s proposal – Merced and Stanislaus – farmers irrigated about 110,000 acres of alfalfa in 2015. Alfalfa is California’s thirstiest crop, and much of it is exported to feed livestock in other countries.

If these two counties simply stopped growing alfalfa, it could free up a half-million acre-feet of water annually. The water board estimates its proposed streamflow increases will cost water users about half this amount.

The water board was careful to express its desired streamflow as a percentage. This recognizes “unimpaired flow” must change with the weather, the season, and the presence or absence of drought – as nature intended.

Muir, a close observer of the natural world, saw this during his 1877 voyage. When he passed through on his way to the mountains earlier, in October, the San Joaquin was “nearly dry” in places and salmon were holding in the river, waiting to move upstream.

“A month ago while evaporation was much greater,” he wrote, “the San Joaquin was in most places a series of currentless pools separated wholly by sand bars. Now quite a current.”

This debate isn’t just about salmon. It’s about improving water quality in the Delta for all the species that live there, restoring riparian habitat on the San Joaquin and its tributary streams, and bringing back a fragment of the free-flowing rivers that made the state a utopia for people and agriculture in the first place.

It is important to remember that rivers and groundwater are connected. Much of the water ordered back to the river will seep into groundwater aquifers. And it will probably be pumped out later by some of the farms and cities that now oppose the flow increases.

When the state’s Sustainable Groundwater Management Act takes full effect in 2022, it will require groundwater users to adopt permanent measures to recharge aquifers. So we may look back on this process of reallocating streamflows with gratitude.

Even the most ardent supporters of more river flow, like Shutes, recognize it will be a difficult journey. He said the state should offer financial support to farmers ordered to give up water, perhaps to help them adopt conservation measures, like drip irrigation.

“I’m not out to punish the irrigators. Food is important,” Shutes said. “But they have to give up some water, and let’s help them to do that.”

Timing presents another unresolved conflict. The water board is simultaneously weighing a crucial permit for California WaterFix, Gov. Jerry Brown’s $15 billion plan to drill two giant tunnels under the Delta to divert a portion of the Sacramento River. The permit would allow three new diversions along the Sacramento River to serve the tunnels.

As events stand now, that permit is likely to come up for a vote before the board has established new flows in the Sacramento River, a so-called “Phase 2” process that will come after flows are revised on the San Joaquin River.

Grober said Phase 2 also will set new rules for total freshwater outflow from the Delta, a vital step that will impose operating criteria on the tunnels.

But the board ought to make the estuary’s needs primary and settle the issue of water flows first, then tackle the WaterFix permit afterward. This is the only way to understand exactly how much water is available for the new diversions.

Adjusting these streamflows is shamefully overdue. The federal Clean Water Act requires the state to review streamflows every three years to maintain healthy water quality. The state water board holds this responsibility under a custodial arrangement with the U.S. Environmental Protection Agency, and further delay risks having those powers taken away.

Streamflows on the San Joaquin and Sacramento river systems have not been comprehensively updated since 1995. It hardly seems surprising that the Delta environment and its fisheries have been careening toward ecological collapse in the meantime.

Matt Weiser is a contributing editor at and a former Sacramento Bee staff writer. Contact him at