SAN FRANCISCO—One person died, two people were missing and 16 others were rescued from the waters off San Francisco after a pontoon boat carrying 19 people sank Tuesday afternoon, authorities said.

San Francisco Fire Chief Dean Crispen reported the toll and said crews that arrived on the scene near Alcatraz Island found a three-deck pontoon vessel almost fully under water, with the motor still running and leaking fuel.

The waters around Alcatraz Island, once a federal prison and now a tourist destination, attract sailboats and other recreational vessels. It lies in San Francisco Bay about a mile north of the city’s shoreline.

The boating mishap was initially reported as a fire, “but we now don’t have any evidence of that,” Crispen said.

Some of the people were injured from falling into the water, but there were no reports of burns, he said. The person who died was alive when plucked from the frigid waters by rescue crews but later died. A dog onboard also died.

Crews continued to search the water for the two missing with divers, helicopters and 11 vessels, Crispen said.

“Right now we are in full rescue mode,” he added.

All those rescued were taken to Gashouse Cove Marina, a small craft harbor in San Francisco. Three people with injuries from falling from the boat were taken to the hospital, Crispen said.

Fire Lt. Mariano Elias said the vessel, described as a “pontoon pleasure boat,” was about 600 yards from Alcatraz and the emergency call came in just after 3:30 p.m.

Crispen said the vessel was believed to have launched near the St. Francis Yacht Club in San Francisco. A person who answered the phone there said the club did not have any information on what happened.

Video images from a local Fox station showed a Fire Department boat deployed to rescue people who had been on the vessel, which was largely submerged with objects floating nearby.

Live video from the scene showed a man and a woman wrapped in blankets and sitting on a curb before walking to a nearby ambulance. A yellow tarp covered a body on the dock.

The Coast Guard and Oakland police also helped in the rescue, Elias said.

By Olga R. Rodriguez