SAN FRANCISCO (KTVU) -- Leopard sharks along with two other species in the San Francisco Bay are dying by the thousands and environmental biologists are attempting to find out why.
Scientists say a witches' brew of bacterial, viral and fungal toxins is killing vulnerable shark populations in the Bay.
"There's probably been several thousand animals dying," said Mike McGill, a marine biologist at the Aquarium of the Bay on San Francisco's Pier 39. "We're just seeing the ones on the surface that are actually stranding on the beaches."
The Aquarium of the Bay has observation tunnels to clearly show visitors what can't be seen with the naked eye by peering into the Bay's murky waters.
Bay Leopard sharks are suffering the worst losses but they are not the only ones.
"Leopard sharks, bat rays (and) some fin fish like halibut," are dying, McGill said.
Scientists say the dying of the marine life began in the waters around the Peninsula before migrating to other areas.
"It started out in the Redwood City, San Mateo area and then spread from there," said Sean Van Sommeran, founder of the Pelagic Shark Research Foundation in Santa Cruz.
Scientists say leopard shark and bat ray sharks are in their pupping season, a time when the offspring are most vulnerable.
There are "toxic substances in those areas that they're swimming through," McGill said. "It most obviously appears to be a storm water runoff issue, complicated by tide gates in a lot of the inland water ways that would prevent the sharks from egressing or exiting those water ways which are filled with storm water runoff," Van Sommeran said.
A lot of the toxins were washed into the Bay by the drenching rains that fell in Northern California last winter.
The soaking rains added to the woes brought by the dearth of tidal marches, reeds and bay side plant life that filtered out toxins.
"This isn't the first one," said McGill, adding that similar events occurred in 2011 and 2006.
The California Department of Fish and Wildlife is collecting the dead sea life and performing necropsies to establish protocols to reduce the loss of marine life.
Officials also hope that restoring more tidal marshes in the Bay Area will help clean the Bay.
By KTVU reporter Tom Vacar.