A new and improved tool that tracks salmon survival in Lagunitas Creek was installed on ranchlands west of Point Reyes Station last month, potentially changing the way the Marin Municipal Water District manages the watershed. 

Every year, ecologists implant a rice-sized microchip in hundreds of juvenile coho salmon. Now, antennas anchored at the mouth of the creek will register their passage when they swim to or from the ocean. Scientists will use the data to understand the relationship between where salmon grew up and how they fared in the sea.

“This tool will answer some questions that will hopefully take our environmental enhancement work in a different direction,” the district’s aquatic ecologist, Eric Ettlinger, said. “We know a lot more than we used to, but there’s still a lot we don’t understand.”

The antennas replace a makeshift system built in 2012 that was inaccurate and easily damaged. Funded by $27,000 from Trout Unlimited, Marin County and the Marin Agricultural Land Trust, the new system was built on the Gallagher Ranch, a mile upstream from Tomales Bay. Its two antennas were covered in pipes and placed in shallow waters outside the range of interference by a nearby power transformer, which hindered the previous iteration. The upgraded antennas are stronger and more reliable.

How salmon survive in the Lagunitas Creek watershed is a puzzle for ecologists like Mr. Ettlinger, and the monitoring system could confirm or disprove some of his theories.

One factor blamed for salmon mortality is a lack of slow-water habitat, so restoration projects involve placing logs and woody debris to slow creek flows. But a more important factor could be a lack of access to smaller tributaries when streams flood, meaning the removal of blockages to such tributaries could be equally important. How much streamside construction plays into survival is another critical yet unanswered question.

The National Oceanic and Atmospheric Administration uses the same technology to track coho in the Russian River watershed, where nearly 100 antennas are deployed. With the region now using the same technology, researchers will also begin to understand how often fish drift from their natal streams.

“The more antennas there are out there, the clearer the picture gets for us as to what these fish are doing,” said William Boucher, a biologist with the Russian River Salmon and Steelhead Monitoring Program.

Salmon born in Lagunitas Creek spend a year and a half in freshwater before migrating to the Pacific Ocean through Tomales Bay. After another year or two, they return to their birthplace to spawn. In the watershed’s best seasons, ocean survival reaches 10 percent; in recent years, it has averaged 4 percent.

Land managers are resigned to the idea that ocean survival lies mostly outside their control. “The best we can do is allow the fish to survive and grow as much as possible while they’re in the creek. Then they’re on their own when they go to the ocean,” Mr. Ettlinger said. 

Todd Steiner, the executive director of the Salmon Protection and Watershed Network, agrees. His organization uses many tools in the conservation toolbox: research and monitoring, the repair of land-use mistakes, land acquisition and policy advocacy to protect streambanks.

Coho salmon on the California coast are endangered, pushed to the edge by habitat loss, ocean fishing and a changing climate. NOAA estimates the population was in the hundreds of thousands in the 1940s, but by the 1980s the species was on the brink of extinction, with fewer than 3,000 wild fish spawning each year. Since then, the species has just barely recovered, thanks to hatchery programs, fishing protections and habitat improvements.

“At best, we’re treading water in allowing them to be extant here,” Mr. Steiner said.

Marin carries roughly 10 percent of the state’s population of coho, and both public and private sectors have spent millions of dollars on heavy-duty construction projects to promote their survival. But the fish continue to struggle. NOAA set a recovery target of 1,300 nests in the watershed; biologists have surveyed an average of 250 nests since 1995. Only 50 were counted last year.

The Marin Municipal Water District was required to steward the watershed after damming the creek to form Kent Lake in 1953. The district oversees annual fish counts, with scientists and volunteers perusing the bank and looking for salmon at each stage of their life.

So far, this year is looking good for a healthy run. The cohort that migrated a year and a half ago and is set to return was abundant, and fisherman have reported accidentally catching coho while casting for chinook or halibut. “That’s a really good sign,” Mr. Ettlinger said. “It sounds like there are a lot of coho in Tomales Bay waiting for the rain to make their trip up to Lagunitas Creek, so I’m pretty optimistic.”