Low Coho returns to Issaquah Creek have redefined what the Issaquah Salmon Hatchery thinks of when it talks about bad years.

Typically a bad year means only a few thousand of the fish returned for spawning. This year only 280 fish made it back to the hatchery.

The numbers have baffled biologists, who can only guess at what might have caused the low returns.

“I’ve been here eight years, and haven’t seen anything quite like it,” said Gestin Suttle, executive director for Friends of the Issaquah Salmon Hatchery. “Something has happened to them, but nobody has a good answer.”

The hatchery collected about half a million fertilized eggs about 1.2 million short of its requirement. It plans to truck in the remaining eggs from the Wallace Creek Hatchery in Sultan.

The best guess at what happened to the Coho came from a Muckleshoot Tribe biologist Mike Mahovlich, who points to a change in ocean upwelling in 2009.

Upwellings, which bring nutrients to the surface to help feed fish, stopped late summer and early fall in 2009. It’s like a desert for fish.

That fall few juvenile Coho could be found, the first indicator that the adult returns would be low the following year, he said. “At that point, people were hoping the fish were somewhere else.”

Only 3,608 of the 30,000 expected Coho returned through the Ballard Locks this year, and there are even some questions about what happened to salmon who made it through the locks, Suttle said.

Heavy rains cause freshets, which can cause the salmon to stray off their old routes, but even still Mahovlich was surprised by how few made it back.

“It’s all theory, because nobody seems to know for sure” Suttle said. “There are so many things that come into play when you talk about the survival of salmon.”

Mahovlich suspects the event will also affect next year’s three-year Chinook returns and the following year’s four-year Sockeye returns.

“Right now, it hasn’t just affected just one species,” he said.

While the overall Coho returns were low, there was a high return of jacks, salmon who return a year early, indicating a good year for Coho in 2011.

Unlike last year’s calm El Nino weather, this year’s La Nina promises stormy weather, which is good for fish, Mahovlich said.

Starting a pilot program last year to bring back the Lake Sammamish Kokanee, the hatchery launched a full-bore effort this year, Suttle said.

About 29 fish were spawned from two creeks, totaling about 15,000 eggs. The goal was collect 110,000 eggs to help revive the species.

Meanwhile the Chinook had a typical, but strong return. The Issaquah hatchery spawned more than 1,000 Chinook and released more than 1,000 king salmon upstream.

In an unassuming white trailer on the hatchery property, a group of contractors snip the andipose fins off more than 500,000 Coho in preparation for their release in the spring.

Removing the fins separates the hatchery salmon from the wild fish, which are sometimes illegal to keep.

Picking up the strong but small fish, each worker hand snipped about 1,000 fins a day.

Nick Samargis snips the andipose fins off of Coho Salmon at the Issaquah Salmon Hatchery. Workers snipped about 1,000 fins a day.

Celeste Gracey/Issaquah Reporter

Nick Samargis snips the andipose fins off of Coho Salmon at the Issaquah Salmon Hatchery. While spawning returns were poor this year, the hatchery plans to release 500,000 Coho in the spring.

Celeste Gracey/Issaquah Reporter