West Marin Compost is succeeding at most of the goals it set out to accomplish: limiting greenhouse gas emissions, removing pollutants from watersheds and eliminating fuel for wildfires. But it has not succeeded at breaking even. 

The operation mixes garden clippings, horse manure, cow manure, brambles, branches and entire fallen trees into a varied menu of organic fertilizers and mulches. Its products sequester carbon and boost the health of gardens, grasslands and farms around West Marin.

The compost drop-off location is around the bend from the Nicasio Reservoir, on parcels owned by Marin County and Marin Water. The ingredients are mixed and seasoned at a ranch a half-mile down Nicasio Valley Road. The enterprise is a public-private partnership between Kevin Lunny, a Point Reyes businessman and rancher, and the Marin Resource Conservation District. It was launched with high hopes and much fanfare in 2012.

But Mr. Lunny has concerns about its economic sustainability, and his recent effort to prop it up financially by opening a lumber mill led to a standoff over zoning rules with the Community Development Agency.

Mr. Lunny installed the mill last year and began making lumber from some of the increasing number of large trees left for composting at the site. He sold it to furniture makers and others, hoping the modest profits would allow him to close the $50,000 annual deficit the compost enterprise has run for several years.

But when the planning department received an anonymous noise complaint last year, it ordered Mr. Lunny to shut down the mill while it investigated.

“We love this business,” said Mr. Lunny, who owns the composting operation with his wife, Nancy. “We love the role it plays for the county. It’s solving a lot of problems. Yet we can’t afford it. We’re in the red. We’ve been in the red every year since we started, and we need a solution.”

After investigating the complaint, the agency concluded that mills are not permitted in the planning zone where the compost operation is located. Now, the mill’s future is in the hands of the C.D.A. and the Marin Resource Conservation District, which provided start-up funding for the project and serves as co-lessee of the property. 

If Mr. Lunny’s business were strictly a private operation, it would have no chance of reopening. 

But the county can suspend zoning rules for projects on its lands—indeed, it did so for the composting operation. Mr. Lunny is hoping it will do so for the mill, which he says is significantly quieter than the grinding of green waste into compost. 

“We believe the mill is absolutely in keeping with the original goals, spirit and intent of the compost project,” he wrote in a letter to the R.C.D. in December. “Milled wood products can sequester carbon for decades or even centuries, while milling itself is a much less labor-intensive process than grinding.”

The mill is housed in a three-sided shed, roughly 12 feet wide and 14 feet tall, and contains a large band saw capable of cutting trees with a diameter of up to 70 inches.

Mr. Lunny did not notify the R.C.D. about the mill operation until after the planning agency shut it down. Nancy Scolari, the conservation district’s executive director, said the board will soon discuss whether to support the mill or consider another way to sustain the compost operation. She wants to see it continue.

“All parties were on the same page about the compost project,” Ms. Scolari said. “The county wanted to reduce the amount of green waste being hauled over the hill, deal with water quality impacts at ranches and reduce greenhouse gas emissions. That was the intent, and all those things were accomplished.”

Since the project began, she said, three West Marin ranches have established on-site composting operations of their own to promote the health of their farmland. The R.C.D. has lined up $2 million in funding, some of it from Measure A, to help other ranches set up similar operations in the coming year, she said. Unlike West Marin Compost, the others will not be commercial enterprises.

Sarah Jones, the interim director of the Community Development Agency, said her department will conduct an environmental impact review if the R.C.D. decides to endorse the mill. If it passes ecological muster, it could conceivably resume operations.

“We would all have to work together to find a way for this use to exist that’s not going to create environmental issues,” Ms. Jones said. “We would need to problem-solve together on this.”

West Marin Compost faces some unusual economic challenges, Mr. Lunny said. Competing operations in Novato and San Rafael have their drop-off locations and composting sites in one place, whereas West Marin Compost’s drop-off spot is a half-mile away on a private farm.

Grinding the green waste at one spot and then hauling it to the other for pickup costs about $150,000 a year, Mr. Lunny said. 

There are additional factors that limit potential profits. If the operation raises drop-off fees or the price of its fertilizers, customers will drive over the hill in search of cheaper options, Mr. Lunny said. Meanwhile, the volume of green waste left by the county, which pays discounted drop-off fees, has grown dramatically in the last few years due to increasingly intense storms in the region.

Additionally, a push by the county, the state and Pacific Gas & Electric to reduce fire accelerants has tipped the balance of brush and trees arriving at the site, with many more trees than in the past. Producing organic compost requires a particular mix of carbon and nitrogen, and adding too much wood destroys the balance, Mr. Lunny said. 

“If you keep adding wood, it won’t compost and it won’t pass organic standards,” he said.

The mill, which did not handle any wood from commercial companies, employed three people who also produced some finished items, including tables and fence posts. The operation might have generated enough to eliminate West Marin Compost’s deficit and perhaps generate a small profit. 

Mr. Lunny said he and Nancy took on the composting project because they thought it would benefit the county. They already owned a nearby quarry and had much of the heavy equipment needed to grind and compost green waste.

“We’d love to make money, but we knew going into this that it was not going to buy our retirement,” he said. “We knew it was going to be tough, but we didn’t anticipate having to subsidize it every year. It’s really tough.”