Alarmed biologists are trying to figure out why leopard sharks are dying by the hundreds in San Francisco Bay this year, the largest die-off of the striped fish in six years.

Huge numbers of dead sharks, some bat rays and a few halibut have been found since mid-March along the shorelines of Redwood City, Foster City, Alameda, Hayward, Berkeley, Oakland and San Francisco, according to researchers. Some dead sharks and rays were also found on beaches in Bolinas, in Marin County.

It is the second year in a row that large numbers of the bay’s most abundant shark have been going belly up during the spring pupping season. Experts believe the sharks are picking up toxins in stagnant saltwater marshes, sloughs and behind the gates of the man-made lagoons in Foster City and Redwood City.

“My estimate is that several hundred sharks have already died,” said Mark Okihiro, the senior fish pathologist for the California Department of Fish and Wildlife, in a written synopsis. “There appears to be no leveling off of shark deaths in the bay. I am still getting reports from locations throughout the South Bay regarding dead or dying leopard sharks.”

Okihiro said there have been dozens of reports of dead sharks. He collected 21 leopard sharks and two bat rays in April along the Foster City shoreline.

Sean Van Sommeran, executive director and founder of the Pelagic Shark Research Foundation, said he has responded to hundreds of reports of dead fish along the shore this spring and believes the number of dead and dying sharks in the bay could be in the thousands.

It is the largest leopard shark mortality event since 2011, when more than 1,000 dead sharks were counted inside and outside the Redwood Shores Lagoon and along Richardson Bay, in Marin County. Okihiro said sharks do not have lungs and therefore sink immediately to the bottom after death, meaning the numbers that wash up are generally well below the actual number of deaths.

“This is just the tip of the iceberg,” Van Sommeran said. “We’re only seeing a fraction of the actual losses.”

The problem, according to Van Sommeran, is that leopard sharks come into the shallow waterways to mate and pup during the spring and summer. Experts believe the sharks are getting stuck in man-made lagoons in Foster City and Redwood City when those cities close their tide gates during low tide.

The cities close the gates at low tide ahead of heavy rains so that the extra precipitation doesn’t combine with high tides and flood homes along the water. The fungal blooms that form in the stagnant water suck out the oxygen and poison the fish.

“If leopard sharks are trapped within these stagnant waterways with high levels of suspended fungi, then they could be exposed to an overwhelming number of fungi, become infected and die,” Okihiro said. “Leopard sharks in the bay proper are likely exposed because they aggregate in large numbers, in shallow water, during the spring.”

Van Sommeran thinks the rainy season exacerbated the damage by washing out toxins that accumulated in the ground during the recent drought.

“With the hard rain there’s extra crud going into the watershed,” Van Sommeran said.

Shark die-offs have occurred often in the past. More than 700 sharks and rays washed up in Alameda in 1967. Die-offs were also reported every year between 2002 and 2006, and then again in 2016. The biggest known shark death toll was in 2011.

Leopard sharks were once so common that they would be seen as far away as Sacramento. Tiburon, the Spanish word for shark, is believed to have been named after the leopard shark, which once grew 5 to 6 feet long and lived four or five decades, Van Sommeran said.

They aren’t endangered, but they were regularly caught by bay fishermen until the 2011 die-off, when state regulators warned people not to eat them because of accumulated toxins in their blood and meat.

“It’s the signature species in San Francisco Bay,” he said. “If they keep losing these numbers every spring when they are trying to pup, that’s asking for disaster. They can’t sustain these losses.”

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