The recent rains have been a blessing for most of West Marin’s farmers, but not for those who harvest their crop from Tomales Bay. The procession of atmospheric rivers has forced a series of closures that have disrupted their oyster supply and their cash flow. Rain closures happen every winter, but this year’s storms forced longer closures than usual. The shutdowns typically last for four or five days, but this year, parts of the bay have been closed for three or four weeks at a time. “This may not be the record year, but it’s close,” said Terry Sawyer, co-founder of Hog Island Oyster Company, which so far this year has harvested for just one week in January and six days in March. Tomales Bay oyster farms must stop harvesting each time it rains a half-inch or more to test for fecal coliform bacteria carried down from ranches in storm runoff. The levels are closely monitored by the California Department of Public Health, which sets limits for closures. The two biggest operations, Hog Island and Tomales Bay Oyster Companies, have temperature-controlled water tanks that can hold oysters after harvesting. But Hog Island, which operates several oyster bars around the Bay Area, ran out. “We have needed to order oysters from farms in the Northwest and some East Coast farms that we know and trust for quality,” Mr. Sawyer said. The last of the recent closures, which began on March 28, ended this week. Tomales Bay Oyster Company had enough oysters in its tank to ride out the shutdown, but business was down sharply, as fewer people ventured out during the storms. The rain, tides and runoff have varying impacts on different parts of the bay, which is divided into six oyster farming zones. “We had an area that was open for one day last week, and then everything got closed again,” said Heidi Gregory, who manages T.B.O.C. “We’ve been closed for a month in some areas, but we were able to harvest there and put some oysters in our tanks. We watch the weather like hawks and try to see the exact timing of things.” Hog Island typically harvests about 3 million oysters a year, while T.B.O.C. harvests around 1.6 million. Mr. Sawyer and Ms. Gregory said there’s still plenty of time left in the year to hit those targets. “We won’t know how it’s going to affect us until the end of the year,” Ms. Gregory said. “Things will pick up and start moving along pretty soon.” In addition to bacteria carried by runoff, heavy rains pose other threats to oyster supplies. Sediment stirred up by storms can bury oysters, and too much freshwater in the bay can kill them. Mr. Sawyer said Hog Island has had some oysters buried by sediment and is currently assessing the extent of its losses. For smaller companies that don’t have holding tanks, storm impacts have been especially great. Starbird Mariculture, a smaller producer that sells oysters to restaurants in San Francisco and Santa Rosa, had to stop deliveries for three weeks, said the company’s owner, Chris Starbird. Short-term interruptions are damaging to cash flow, but falling salinity levels are a potentially bigger concern. “It’s the mortality related to freshwater that we worry about,” Mr. Starbird said. The impact of lower salinity isn’t immediately evident because it kills oysters slowly. “We have seen a small amount of mortality showing up for one reason or another, and that could turn into more and more,” he said. “Like every animal, oysters have a chemistry, and their chemistry is balanced in water that has salinity. They’re okay for awhile, but if the level drops for extended periods of time, they don’t make it.”