State and federal wildlife officials are scrambling to figure out how hundreds of endangered salmon recently became stranded in irrigation ditches in the Colusa basin, west of the Sacramento River.
Finding the answers is a matter of some urgency, because tens of thousands of fall-run Chinook salmon are weeks away from their annual return from the ocean to the Sacramento River and could also become trapped.
"There has been some stranding in the past, but as far as I can tell, the numbers have been significantly lower than this," said Jeffrey McClain, assistant supervisor at the National Marine Fisheries Service office in Sacramento. "It's significant, and that's why this is a serious thing for us to figure out."
The rescues were led by the California Department of Fish and Wildlife. In 11 separate trips over a month, starting May 2, officials rescued 312 adult salmon headed upstream. Of these fish, at least eight were determined to be spring run, and the balance were winter run.
Spring-run are listed as a threatened species under federal law, and winter-run are endangered.
Twenty-four of the rescued fish were missing their adipose fins, indicating they were winter-run salmon bred at the U.S. Fish and Wildlife Service's Livingston Stone Hatchery near Red Bluff.
During the rescues, 18 salmon either died after handling or were found dead in the canals. Many more live salmon were seen but could not be rescued because of flow or terrain obstacles.
Water temperature at some rescue sites was 74 degrees. Salmon begin to suffer when temperatures exceed 68 degrees, and will eventually die from prolonged exposure.
Most of the rescued fish were taken by tanker truck to a release site on the Sacramento River near Butte City.
Kevin Shaffer, salmon conservation manager at the California Department of Fish and Wildlife, said it is possible that many more stranded salmon went undetected in the hundreds of miles of irrigation canals that form a watery maze in the Colusa basin, the agricultural region west of the Sacramento River.
"Basically, the strandings went on for some time," Shaffer said. "I can't imagine all those animals would be able to get out themselves."
Stranded salmon were first seen April 24 by an employee at Sacramento National Wildlife Refuge, which is connected to irrigation canals in the basin. Most of the rescues occurred there, as well as at Delevan National Wildlife Refuge.
The web of ditches eventually drains into the Yolo Bypass through a canal called the Knights Landing Ridge Cut. Officials suspect this is one way the salmon swam astray, probably when the Yolo Bypass flooded after heavy rains in December.
The balance of winter was odd. That wet December was followed by the driest January-through-June in recorded history. This led to unusually low flows on the Sacramento River for most of winter.
As a result, winter-run salmon may have gotten their primary migratory cue from the agricultural canals. That water is diverted far upstream, and because natural runoff in the region was low, the canals may have held a stronger Sacramento River "scent" than the main stem river, which also includes a mix of waters from the Feather River, the American River and other sources.
"The big topic that comes up with this water year is if that attracting flow of Sacramento water is one thing that brought the fish into the canals," said Shaffer. "In a normal water year, the fish do not get off course."
Another possible entry is the Colusa Basin Drain, a large concrete structure with large steel flapper gates, near Knights Landing along the Sacramento River. Under certain flow conditions, drainage from the basin empties here instead of from the Ridge Cut, which is at the north end of the Yolo Bypass.
The California Department of Fish and Wildlife determined there were 23 days in January and February when flow conditions could have allowed salmon to migrate through the drain.
The large number of rescued fish caused officials to worry initially that the strandings could jeopardize the entire winter-run population.
So 48 of the rescued salmon were taken to Livingston Stone Hatchery to breed them artificially as insurance. A subsequent report by the National Marine Fisheries Service indicated that 13 of these salmon died before they could spawn.
McClain said this year's winter run eventually proved to be larger than expected, so he does not think the stranded salmon represent a significant share of the population.
"It's doesn't mean we're not concerned," he said. "Every one of these fish is important."
The strandings frustrate conservation groups, which have complained for two decades that fish can be trapped in the vast canal and bypass systems fed by the Sacramento River.
"This is an indefensible failure to protect species hovering on the brink of extinction," said Bill Jennings, director of the California Sportfishing Protection Alliance.
In 2011, for example, more than 200 endangered green sturgeon, spring-run salmon and steelhead trout were rescued from the Yolo and Sutter bypasses. Many others were not rescued and perished.
There is an antiquated fish ladder at the Fremont Weir in the Yolo Bypass, but it is known to be impossible for many species to navigate, especially during low flows.
The U.S. Bureau of Reclamation is required to fix these fish passage problems and is preparing an environmental impact report on the project. Fixes may include a new fish ladder at Fremont Weir and a structure at the Knights Landing Ridge Cut to exclude fish.
In the meantime, efforts are underway to prepare for the arrival of fall-run Chinook salmon in just a few weeks. This run is not yet protected by the Endangered Species Act. But it underpins California's commercial and recreational salmon fishery, so it is closely watched because its numbers have been volatile.
Shaffer said his agency hopes to install special underwater cameras in the next few weeks at the Ridge Cut and Colusa Basin Drain to figure out where the fish are getting in. The cameras capture detailed images using sonar, allowing officials to identify fish by species even at night and in muddy water.
It will also be ready, with people and equipment, to rescue more fish if necessary.
Contact The Bee's Matt Weiser at (916) 321-1264. Follow him on Twitter @matt_weiser.