For the second summer in a row, healthy juvenile coho salmon have been spotted in Pine Gulch Creek, more than tripling last year’s count. Biologists say the numbers represent a recolonization of a habitat abandoned by the species since 2010.

Fishery crews have observed over 300 coho, and four nests, though the true count is likely around 1,000 fish, said Michael Reichmuth, a fisheries biologist for the National Park Service. The raw count represents numbers in a portion of the creek, measured using electrofishers that stun the fish for easy capture and weighing. Formulas are then applied in tandem with habitat data to yield a truer number.

Mr. Reichmuth said coho were once native inhabitants of Pine Gulch Creek but were extirpated due to damming and a drought in the late 1970s. Surveys of the creek found no coho in the ‘80s and ‘90s, and it wasn’t until the park service started salmon monitoring in the early aughts that coho were observed again. Yet populations slowly crumbled in the following years.

The young coho seen this summer are the offspring of spawners that returned to Pine Gulch earlier this year, which were part of the cohort observed last year that numbered around 80. Biologists say it is likely that the population originally came from a nearby source like Lagunitas Creek or Redwood Creek.

Although there is no guarantee that the cohort will establish a long-term population, Nancy Scolari, the executive director of the Marin Resource Conservation District, says it is promising to see these fish growing in a supportive habitat.

A healthy watershed is essential for the survival of young coho, which need deep pools during the summer.The juveniles will spend a winter in the creek’s freshwater before moving out to the ocean for 18 months and then returning to spawn again.

The restoration of the Pine Gulch Creek population comes almost two decades deep into a project spearheaded by the Marin R.C.D. aimed at creating a more hospitable environment for salmonids.

The project, conceived in the late ‘90s and implemented in 2015, involved three farms handing over their rights to pull water from the creek from July to mid-December. In exchange, the R.C.D. facilitated the creation of small ponds on the farms, increasing water storage for the agricultural operations and their resilience to climate change. Under the agreement, the farms—Peter Martinelli’s Fresh Run Farm, Dennis and Sandy Dierks’s Paradise Valley Farm and Star Route Farm, then owned by Warren Weber—could pull water from the creek during the rest of the year.

The project was initiated by the park service, since the creek, which starts north of Dogtown, runs through the Point Reyes National Seashore before emptying into Bolinas Lagoon. But it was taken over by the R.C.D. about 15 years ago when a re-evaluation of its scope paved the way for a more extensive plan that required a greater sequestering of water.

“That really was a shot in the arm, because the R.C.D. is a more appropriate agency to coordinate different permitting processes and gather funding,” Mr. Martinelli said. “Once they came on board, the project got re-energized.”

Obtaining the permits and funding to build the ponds was a major effort involving federal, state and county agencies, so having the right organization backing the effort was essential, Mr. Martinelli said.

“The project took 17 years to pull together, and the farmers have endured through that time,” Ms. Scolari said. “It was a very innovative project. At that time, no one was relinquishing their water rights for the greater good of the fish, which is what those farmers did.”

The project cost $3.3 million, with $2.4 million coming from the Fishery Restoration Grant Program, a competitive grant administered by the California Department of Fish and Wildlife to areas with rapidly declining fish populations. In the most recent cycle, just $16 million was awarded to projects and as contingency funds. Another $20,000 for the Pine Gulch project came from an anonymous donor, and $47,000 came from landowners.

According to the R.C.D., the project achieved a number of feats. The reduced agricultural use of the creek resulted in increased streamflows, a sequestering of carbon over time and the reintegration of endangered red-legged frogs, with around 500 red-legged frog tadpoles showing up in Mr. Martinelli’s ponds the first year.

“There are so many factors, including climate change, ocean conditions and so much more, that affect watershed conditions,” Ms. Scolari said. “So we are feeling very encouraged to see these numbers and are optimistic for the future.”