The water is back, but the fish are not.

Recent rains have reinvigorated creeks throughout Marin County after a bone-dry January.

But federally endangered coho salmon are at their lowest total in the county since records were first kept 15 years ago.

"It's abysmal," said Greg Andrew, fisheries biologist with the Marin Municipal Water District. "These are the lowest totals we have seen."

Biologists have counted 43 coho salmon and 26 redds - clusters of eggs - in Lagunitas Creek, San Geronimo Creek and Devil's Gulch. On average there are 557 fish and 229 redds spotted by now. Only one redd was found in San Geronimo Creek.

It is the second straight year of low coho counts, and with the coho spawning season essentially over, this winter looks to be the worst on record.

"We were hoping after the last rains we might see some more activity," Andrew said. "But we haven't seen anything."

The story is the same at Muir Woods, where for the second time in two years no coho have been seen in Redwood Creek.

"We are crossing our fingers that one or two slipped in, but so far we have not seen anything," said Mia Monroe, Muir Woods superintendent. "It's grim."

Andrew blames a "multiple whammy" of impacts on this year's class of fish.

Coho salmon have a three-year life cycle in which they hatch, live in creeks for a year and go to sea for two years before returning to their birth sites. This year's returning adults were hatched in the winter of 2005-06.

On Dec. 31, 2005, a flood that devastated the Ross Valley flushed out many of the redds that were in creeks, Andrew said.

Additionally, in March 2006 as the juvenile coho were emerging there were heavy rains that washed out fry.

"The ones that made it through the flood got hit with high flows," Andrew said.

Those that did survive made it out to the open ocean the next year.

"In 2007 there were poor ocean conditions," Andrew said. "That basically means there was a poor food supply and many of the coho that did make it out became food themselves."

And the recent dry January - a little over an inch fell on Mount Tamalpais - meant there wasn't as much water in creeks as coho made their way back upstream.

Small tributaries such as Arroyo, Larsen, Woodacre and Willis Evans creeks in the San Geronimo Valley have traditionally made up as much as 30 percent of the coho population.

"This year we saw nothing in the tributaries," said Christopher Pincetich, watershed biologist for the Forest Knolls-based Salmon Protection and Watershed Network. "It was a first."

The issues seen with coho in Marin this year are being mirrored in other parts of the state as well.

"It seems pretty much the pattern that the coho numbers are down this year," said Bill Cox, biologist for the state Department of Fish and Game, citing the lack of January rain.

"By the time the rains started in February the coho runs were generally over with," Cox said. "The coho has a very rigid life cycle, and that has hurt them."

In Marin, that is less of an issue because the Marin Municipal Water District releases water from its reservoirs down creeks per an order from the state, although the volumes are not levels a storm would produce.

Marin's salmon run is one of the more critical in the state. The Lagunitas watershed has one of the largest remaining populations of wild coho salmon in Northern California. Coho have gone extinct in 90 percent of California streams that once supported the species, usually because of development along creeks that fills them with sediment.

Last year's low numbers were never fully explained, although changes in ocean patterns possibly due to climate change and even the Cosco Busan oil spill may be having an effect, experts said.

There is a chance this year's class could bounce back if a large number of the juveniles that emerge this month are able to survive and make their way back out to sea.

The water district and groups like the Salmon Protection and Watershed Network are working to maintain and improve Marin creeks to make sure fish can survive.

"The Lagunitas system is still one of the best in the state," Cox said. "Despite the history of a railroad practically running through it and logging, it still holds the best chance for a good future."

Contact Mark Prado via e-mail at mprado@marinij.com