James Smith, a veteran seaman and captain of the charter fishing boat California Dawn, was sailing his vessel under the Golden Gate Bridge on Tuesday when he heard the call on his radio: A vessel was in distress near Alcatraz Island.

From a distance, Smith saw what looked like steam or smoke rising from a speck in the water. As he sped to the scene, he saw that a large motor boat was rapidly sinking. Some passengers were frantically clinging to the hull of the partially submerged vessel, he said, as rescuers administered CPR to a man on a San Francisco police boat.

“Something went catastrophically wrong with the boat to make it go down like that,” said Smith, who has operated charter boats for 35 years. “It wasn’t just because a wave hit it and it just turned over.”

Rescue teams scrambled to pull 17 people to safety, but after reaching the shore the man who was given CPR was pronounced dead. On Thursday, a female passenger was recovered from the bay and pronounced dead. Two passengers remain missing.

As search teams continued to scour the bay Thursday to find the missing passengers and recover the wreckage of the sunken vessel, it is not yet clear what caused the 49-foot boat with three levels to roll on its side and topple into the water.

According to Capt. Jarod Toczko, the U.S. Coast Guard’s San Francisco sector commander, survivors of the incident reported that a wave hit the boat, causing it to list heavily and suddenly roll over.

But maritime investigators and experts, including the captain who was out in the bay that day, told The Times that a single wave was unlikely to cause such a large cabin cruiser to sink. While the exact cause will not be determined until officials retrieve the boat from the ocean floor and conduct a full investigation, they said the vessel, which was carrying 20 passengers on a memorial to honor a loved one, most likely took in water after a series of cascading issues or failures.

Although the water was choppy Tuesday afternoon, Smith said, it was not extremely rough. He estimated there was maybe a 4-foot wind chop and said smaller vessels out in the water fared fine. In such conditions, a 49-foot boat would typically be stable and 20 passengers wouldn’t be expected to overload it.

This particular boat, he noted, had already ventured out to rougher waters earlier that day — passing under the Golden Gate Bridge to the Pacific Ocean before coming back across the San Francisco Bay to Angel Island — before returning to the more protected bay waters.

A number of factors, Smith said, could have caused the vessel to take in water as it headed back to a San Francisco marina. The boat — called Volare — could have lost the water line that cools the motors, he said, or lost the metal shaft that transfers the engine’s rotational power to the propeller to drive the boat forward.

“My guess is he lost a line to his cooling,” Smith said, referring to the raw water line that pumps water in to cool the motor and sends it back out the back of the boat. That, he said, might explain the steam rising from the boat. On a boat that size, he said, the line would probably be about 1½ or 2 inches thick.

“A 2-inch hole in your boat, it doesn’t take very long to start filling up,” Smith said. “You’re on a cruise, you got a bunch of people, a bunch of noise, maybe the boat’s rocking and you don’t even notice it before it’s just too late.”

Randell Sharpe, a marine accident investigator in the Bay Area, agreed that a wave probably did not cause the boat to sink. More likely, he said, there were multiple compounding factors.

“For a vessel that size to basically be overcome, it’s not going to be just a single wave,” Sharpe said, noting that photos and videos from the scene showed the water was rough, but not severe enough to overturn a large motor boat.

The waves could have gotten the vessel to oscillate back and forth, Sharpe said. But even then there would have to be openings — in the portholes or sides of the lower cabins or some failure in the engine room — that allowed a lot of water in and made the boat lose stability so quickly.

One photograph of the boat, he said, shows seven windows along the side below the main deck. If the windows were open, he said, the boat could have suddenly taken on a tremendous amount of water once it started rolling.

“Were the windows open?” Sharpe said. “Do they find some other source of leakage in the engine room, possibly a hose that goes to one of the engines, or just a drain hose, or something that allowed water to come in from below the waterline?”

If there was a problem, he said, the distribution of passengers on the boat might exacerbate the problem: a lot of people up top would make the boat more top heavy.

According to survivors, Toczko said, some passengers were below deck but many were on the main deck when it ran into problems.

“Was everybody standing on the same side of the boat, looking at the city front?” Sharpe said. “That would worsen the stability of the vessel, so you tend to tip more in that direction.”

After looking at the boat’s tracking data, Capt. Jim Elfers, a marine surveyor in the Bay Area who provides damage inspections and yacht safety evaluations, said that as the boat came out of Angel Island’s Ayala Cove, heading back toward the city front, it might have fallen victim to a cascade effect called the “beam sea effect.”

“It’s a cyclical roll that gets set up when a boat is taking even a 4-foot wave cyclically over and over on the beam,” Elfers said, referring to the widest point of a boat’s hull. “It sets up a roll, and in this case, the center of gravity on this boat may have gotten very high. If you have [20] passengers on a 50-foot boat, especially if they’re all the way at the very top deck, you’ve got the center of gravity going up high. You’ve got the boat getting into a cyclical roll.”

If one big wave managed to get onto the decks, which is not unusual in the San Francisco Bay, Elfers said, that could present problems if the boat was not watertight: Water would find its way to any little compromised area or anywhere that’s not sealed and get into the hold and start a cascade of negative effects that could make the boat less stable and slightly lower in the water.

“And the next wave comes, the next wave comes, and all of a sudden you’re capsizing,” Elfers said. “It’s kind of like when you have a child on a swing, you can push that child with two fingers slowly, but slowly you can get to the point where you’ve really got a roll going on that swing.”

After being a licensed captain for 35 years, Elfers said he was always careful, if he started to notice a beam sea effect and had a lot of passengers high up, to move people down into the cabin.

“You normally would get a little warning, because the boat’s starting to roll, but it hasn’t gotten horrific yet,” he said. “That’s the time when you’re trying to move people and weight down. I personally would have said, ‘Hey, look, it’s going to get a little roll-y here for about the next 20 minutes. I need half of you, or all of you, to go down lower in the boat.’”

Elfers also said it was very common for a boat engine, which does not have a closed cooling system like a car, to have a hose that pops or a hose clamp that fails.

“Something fails, and the engine itself starts to pump water into the engine compartment,” he said. “That’s very common because the engine is sucking constantly from the ocean to cool the engine.”

It’s unclear how thoroughly the boat, which was documented in Stockton, was maintained or inspected before this week’s voyage.

According to the San Francisco Chronicle, John Boisa, 62, owned and captained the vessel. He was a younger brother of Clifford Joseph Boisa, the passenger who died in the incident. A family member told media outlets that his brother was an experienced seaman.

“He was an officer in the Navy and he knows how to handle a boat,” his brother, Ralph Boisa, told CBS News. “He’s been out on the bay and through the Golden Gate and down the coast many times without any mishap of any kind.”

Smith said he could only guess about the maintenance of the boat or the captain’s experience, noting that it was a private vessel.

“I hate to speculate because boats, they can sink in a moment’s notice,” Smith said, noting that he had “all kinds of weird stuff” happen in his 35 years at sea. “Some kind of fluke could have happened.”

People should always be cautious when they’re out on the water, Sharpe said.

“You have to do regular maintenance constantly on a boat,” he said. “It’s not, like, a car that you can take it in every six months or once a year for an oil change.”

“Until the Coast Guard raises the boat, or they come out with some other preliminary investigation, it’s anybody’s guess.”

On Thursday, divers from the San Francisco Police Department’s Marine Unit, coordinating closely with the U.S. Coast Guard and other partners, conducted a grid search for the vessel, which is believed to be about 120 feet deep in a rocky seabed, using boat-mounted sonar platforms and other tools.

Once the vessel has been located and positively identified, the department said in a statement, it will coordinate with the U.S. Coast Guard and other partners to evaluate recovery options and determine whether it can be recovered from the ocean floor.

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