For San Joaquin River revival, drought becomes way of life

In the shallow, gently flowing San Joaquin River, three tiny chinook salmon swim into a trap that saves their lives.

Federal biologists Don Portz and Charles Hueth wade across river cobble at Scout Island to fetch the trio and carefully move them into a tank of water for a truck ride more than 100 miles downstream.

Over the last few weeks, the biologists have trucked nearly 900 young fall-run salmon to where the Merced River empties into the San Joaquin and reconnects this long river to the Pacific Ocean.

The San Joaquin flow goes dry 38 miles beyond Friant Dam -- more than 200 miles short of the ocean where these young salmon need to go. Then, dozens of miles downstream, the connection to the Pacific appears at the Merced River, the first major tributary flowing into the mainstream.

That's the snapshot of the hard-fought and still-debated San Joaquin River restoration project after the driest winter in decades. Forget about releasing water from Millerton Lake and filling dried sections of the river.

As much as controversy swirls around this river, drought is becoming a dominant factor here. The drought is now three years long, meaning the project has spent most of its five years facing dry times.

But it's no time to slow down studies, biologists say. They scrambled to get a close look at how the river and the fish react to this extreme dry time.

"This is an important year to learn about the river," said Portz of the U.S. Bureau of Reclamation. "We need to see how this looks in a critically dry time."

Portz and Hueth, who is also with the bureau, are studying survival numbers, water temperature and flow, habitat condition, diet of the young fish and other factors involved in the restoration program.

But during the driest period in decades, the restoration won't get water from Millerton Lake. Neither will farmers. Is there a chance any of that will change this spring?

Alicia Forsythe, restoration program manager for the Bureau of Reclamation, said: "We have a long way to go in terms of improved hydrology to start releasing water for the program again."

Two or three large storms in Northern California and the San Joaquin watershed would help, says the Friant Water Authority, representing 15,000 east Valley growers who buy Millerton Lake water.

Leaders also say they would need authorities to pump more river water to west Valley farmers through the sensitive and protected ecosystem of the Sacramento-San Joaquin River Delta. Some west-siders have rights to Millerton Lake water, and they may be forced to take the supply this year, leaving none for east-siders.

"It's a long shot to get any supply, but we are still working on it," said Friant general manager Ron Jacobsma.

The east-side farmers have been coping with water losses since the restoration began in 2009 as part of a settlement to an 18-year lawsuit. Farmers reluctantly agreed to the settlement as environmentalists and fishing groups gained the legal upper hand.

The history of restoration goes back to the 1940s when Friant Dam was finished and about 60 miles of the state's second-longest river dried. At the time, the river's water resuscitated a faltering east Valley farm industry spanning 1 million acres. A lot of people depend on the river.

Farmers continue to be critical of the restoration, including west-side growers who have historic rights to the San Joaquin.

One such grower, Cannon Michael, said bypass projects to reconnect the river with the ocean remain underfunded and far behind schedule.

"The projects were supposed to be completed last December, and they haven't broken ground on one of them," he said.

The drought is the focus now. This year, the river goes dry at Gravelly Ford, about 25 river miles from the Mendota Pool. A trickle of water comes from Millerton to supply land owners along the river for a few dozen miles below Friant Dam.

Portz said the young fall-run salmon are the offspring of 367 salmon that were planted in the river at Camp Pashayan last year. The 3- to-4-inch-long fish are caught in V-shaped structures called weirs that allow water to pass but not the fish. The weirs guide the fish to collection boxes.

Portz and Hueth have gathered 1,081 so far and transported 879 to the confluence of the Merced River. (Some fish don't survive the capture and transport process, and some already have died before they are gathered.)

Beyond the Merced, there are many dangerous predator fish and other obstacles, such as pollution. And after the fish mature in the ocean, they must return to the San Joaquin to spawn. It's a perilous journey.

"We hope they come back," Portz said. "How many will make it? Out of 1,000, probably one."

Salmon need cold water to survive, but the river will be warming up, stopping migration for the season. What about the fish that don't make it out in time?

Biologists have learned that some salmon planted in the river in a previous year are surviving around deep, cool pools of water near Friant Dam. Portz said it's an interesting tidbit, especially during a three-year drought.

"This is a resilient fish," he said. "As they grow larger, they become less of a target for predators. It's encouraging to see some of them remain and survive in the river."