Persistently swamped Highway 37 — historically a sore spot for motorists — is rapidly becoming one of the Bay Area’s most pressing issues as heavy storms keep rolling through this winter, forcing repeated closures of a crucial transportation link.

The peculiar highway, which looks more like a rural farm road in places, connects the North Bay to the East Bay by cutting through wetlands and hay fields along the northern shore of San Pablo Bay. Wine Country day-trippers use it, as do drivers headed to Sonoma Raceway and Six Flags Discovery Kingdom in Vallejo.

The increasingly popular artery, which was shut down for much of last week, has been closed for about three weeks this winter because of flooding.

The soggy blockages have raised aggravation levels among tens of thousands of commuters who use Highway 37 each day, and are providing a disturbing glimpse into what ecologists say is a wetter future, in which floodwaters powered by climate change could permanently drown the roadway.

“It is definitely the most problematic area in the Bay Area from the point of view of shoreline flooding and threats to communities and infrastructure,” said Fraser Shilling, co-director of the Road Ecology Center at UC Davis and author of a 2016 report analyzing the future of the highway.

The highway flooded repeatedly last week on a stretch between Highway 101 and Atherton Avenue, next to the Novato Bridge. Shilling said floodwaters caused by pounding rain, unusually high tides and overflow from Novato Creek have been over-topping a berm south of the highway, swamping adjacent pastureland and slopping over a low spot in the highway.

It’s one of several vulnerable locations on the highway that engineers — and locals inconvenienced by floods — have known about for years.

“This is something we foresaw because there are several low spots along these berms and levees,” said Shilling, whose report, Rising Above the Tide, says sea levels have already risen 8 inches along the California coast.

The most vulnerable section, between Highways 101 and 121, could be under water for good if the sea rises another 24 inches, a level Shilling estimates will be reached by 2050.

Low portions between Route 121 and Vallejo’s Mare Island would face permanent inundation with a sea rise of 36 inches, which is the midrange estimate that the National Research Council predicts will be reached by 2100 if carbon emissions aren’t stopped.

The loss of the roadway could be catastrophic for commuters and surrounding communities. But while public officials are studying ways to respond, state Sen. Mike McGuire, D-Healdsburg, said none of the possible answers will be easy or cheap.

One problem is that the highway has sunk in the mud over time. He said as much as 3,000 feet of the highway will have to be raised 3 to 5 feet to get it out of the flood zone.

“This exposes how vulnerable one of the most critical highways in the Bay Area really is,” said McGuire, who met Friday with local and state officials to discuss a proposal for an emergency order by Caltrans to fix the roadway.

David Rabbitt, the Sonoma County supervisor whose district includes the highway, said the four counties divided by the troubled roadway — Napa, Sonoma, Marin and Solano — are working with state legislators on saving the highway.

The most popular idea so far is to build a raised, four-lane causeway that would stretch 11 miles between Highway 121 and Mare Island. This would have the least impact on the environment by getting rid of levees and allowing the bay wetlands to thrive underneath, Rabbitt said.

“For all intents and purposes, Highway 37 has always been like a bridge,” Rabbitt said. “It’s going to be more like a bridge in the future.”

The problem is, a causeway would cost an estimated $4.3 billion and take Caltrans, under its current work schedule, until roughly 2088 to build, Rabbitt said. One option is to turn the highway into a toll road, which would raise money and speed up the work, he said.

“There is probably going to be a toll on Highway 37” at some point, said Rabbitt, a Golden Gate Bridge District director who has had discussions with at least one company that specializes in toll roads.

Highway 37 stretches for 21 miles through marshes, tidelands, rivers and creeks in the four counties. It was originally a patchwork of roads built on levees and ancient Indian trails over what white settlers considered useless swampland.

The Black Point Cut-off, the stretch of road east of Sears Point, was built in 1917 on top of what was once the historic Spanish El Camino Real. Tolls were collected on the road between Sears Point and Vallejo from 1928 to 1938, when it was purchased by the state, according to highway records.

Despite being a state highway, the thoroughfare was a little used two-lane country shortcut until the 1950s when an effort arose to turn it into a freeway. The proposal never came to fruition because of huge costs and environmental issues.

But the roadway eventually became a major artery, and there were so many head-on collisions that people started calling it “blood alley.” Between 1966 and 1970, 27 people were killed on the dangerous eastern section of the highway.

A concrete divider, widened shoulders, passing lanes and new pavement reduced accidents and, as of 2005, there haven’t been any crossover accidents, but the growing popularity of the route also ushered in a new reality: Most of the time, people are inching along too slowly to create much of a wreck.

With continued development and the high price of housing in the North Bay, the road has become a crucial link for priced-out workers living in the East Bay. An estimated 41,000 vehicles use it on any given day.

“We can’t afford to wait for a fix, which is why we need to bring private property owners, the state and county officials together to accomplish the work,” McGuire said.

Peter Fimrite is a San Francisco Chronicle staff writer. Email: pfimrite@sfchronicle.com Twitter: @pfimrite