San Joaquin Valley salmon make small gains against tough odds

12/19/2013 7:59 PM

12/19/2013 9:08 PM

With a flash of silver and pink, a male salmon signaled its arrival in a stretch of the Tuolumne River near La Grange.

It sought to fertilize eggs laid in the shallow stream bed gravel by a female that also had returned from a few years in the Pacific Ocean.

Chinook salmon spawning has been going on since September on San Joaquin Valley rivers. It’s a stirring sight for people who love nature, but important as well to farmers and other water users who could face cutbacks if the fish numbers stay low.

This year, at least, they are not doing too badly. Many of the spawning fish were born on the rivers in 2010 and 2011, when the water ran high, and they enjoyed healthy conditions at sea. They return to streams shrunken by drought, but well-timed reservoir releases have provided some of the flows they need.

“This is where they want to be,” said Gretchen Murphey, an environmental scientist for the California Department of Fish and Wildlife, during an early December visit to the La Grange stretch. “This is the habitat they’re looking for.”

As of Monday, 3,607 salmon had passed through a fish-counting device on their way to the Tuolumne’s spawning stretch in the low foothills, up from 2,152 a year earlier, and just 255 in 2009.

The Stanislaus River had 5,401 returning salmon as of Monday, down from 7,110 last year but much better than the 1,247 in 2009. The counts, conducted at weirs that stretch across the rivers, do not indicate how many of the fish will reproduce successfully.

Salmon used to arrive by the tens of thousands on these rivers each fall, and in far greater numbers on the Sacramento River and its tributaries.

Water diversions to farms and cities have reduced the flows and sometimes made the water too warm for the fish. Gravel mining, pollution and other disturbances have made the rivers less hospitable. Non-native striped bass prey on young salmon in and near the Sacramento-San Joaquin Delta.

“There are so many stresses and so many variables that it’s very difficult to put your finger on it,” said Steve Boyd, director of water resources and regulatory affairs for the Turlock Irrigation District, the largest user of the Tuolumne River.

Flows for fisheries

The TID and the Modesto Irrigation District keep close watch on the salmon as the districts seek a new federal license for Don Pedro Reservoir, a few miles upstream of the spawning grounds. They could be required to boost the river flows beyond what they are doing to aid the migration.

They argue that higher flows make no sense if the salmon are still going to be eaten by bass or weakened by the delta’s poor water quality. “Flow is part of a healthy fishery, but flow alone won’t fix anything,” Boyd said.

MID board member Larry Byrd noted during this week’s meeting that the Stanislaus River has higher flows than the Tuolumne but saw a decrease in returning salmon. “That’s a telling story right there,” he said. “I don’t know that more water makes more fish.”

Fishery consultant Doug Demko said the Stanislaus number could reflect a lower number of hatchery salmon entering the river this year, but the overall trend is positive.

Parts of the west and south valley face drastic irrigation cutbacks from the federal Central Valley Project because of salmon, as well as drought. The giant pumps that send delta water south are blamed for a good part of the fish kill.

Critics warn that further restrictions could cut into the state’s farm production, valued at $44.7 billion in gross income last year. That does not count the ripple effect for suppliers, processors and other parts of the food chain.

A new angle on jobs?

People who catch salmon for a living say there’s more to the story. The Golden State Salmon Association estimates that healthy runs on Central Valley rivers could create $5.4 billion in annual economic activity, compared with $1.4 billion under current conditions. The total includes commercial and recreational fishing, boat and gear suppliers and other businesses.

“We have communities and whole economies that have evolved around harvesting salmon,” said John McManus, executive director of the Petaluma-based group.

It calls for increasing flows and sees value in hatcheries, trucking fish around trouble spots in the delta, and other measures. The group is trying to avoid a repeat of the 2008 and 2009 closure of the fishery off the coast.

McManus said a crucial step is improving “rearing habitat” in the rivers, where young salmon develop before their ocean journey. Some water agencies have done this by restoring natural floodplains, which are covered by water in spring and shaded by trees.

The Oakdale Irrigation District took part in such a project last year at a spot on the Stanislaus River called Honolulu Bar. It involved the U.S. Fish and Wildlife Service and Demko’s company, Fishbio, which has an Oakdale office.

“Because of habitat restoration projects such as Honolulu Bar and others, and favorable conditions for spawning fish this fall, I expect that we will see a significant number of juvenile salmon migrating out of the upper river in 2014,” Demko said by email from the Mekong River in Southeast Asia, where he also consults.

A much larger effort with rearing habitat is in the works in and near Dos Rios Ranch, where the Tuolumne and San Joaquin rivers meet southwest of Modesto.

Tracking the life cycle

Up the Tuolumne near La Grange, Murphey and her colleagues with Fish and Wildlife have been watching over the earliest stage of salmon life. The eggs are laid in spots in the gravel known as redds, in shallow but fairly fast-moving water.

The adults die after spawning, and the crew collects biological samples that are taken to a lab to determine their age. Salmon have parts near their heads known as otoliths with microscopic lines that are similar to tree rings, environmental scientist Crystal Sinclair-Seay said.

Knowing a fish’s age allows scientists to count backward to the year it hatched and get an idea of whether certain practices, such as increased reservoir releases, helped them to survive, she said.

The lab is clean, but salmon counting is a decidedly dirty business. The crew takes measurements of the fish that spawned, some of them dead for several hours, some for several days.

“We still smell it,” Murphey said, “but I don’t think nearly as strongly as anybody else would.”

Experts say the salmon returning this fall benefited from plentiful food and other favorable conditions in the ocean. The 2008-09 fishery closure also aided survival.

But while they were off at sea, California was drying up. The state has gone through two straight years of below-average runoff in the rivers, and it looks like a third is under way.

“We’re worried about the effect of drought on salmon returns in 2015,” McManus said, “and if we don’t get rain this year, we’re worried about 2016.”

Bee staff writer Garth Stapley contributed to this report.

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