More than 120 feet underwater, in the area where it sank on Tuesday afternoon, the three-level vessel was found resting on the rocky seabed. Images released Friday show the exact shape of the boat on the Bay floor.
Experts say sonar technology played a critical role in locating the vessel.
"What is actually doing the mapping is a combination of this and the software. The software is running on the computer, and we also have a GPD attached to it. The GPS is feeding all the coordinates of where we are on the boat while this is painting the bottom. Combine these two together and you an accurate view of the bottom of the Bay," said David McMurdie of California Recovery Divers.
McMurdie and Scott Harrison are expert divers' co-founders of California Recovery Divers, a nonprofit team of volunteers with decades of underwater recovery experience throughout California.
Asked how the scanning process works, McMurdie explained the use of sonar technology.
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"The scanning happens by sending out a sound signal from the transducer on the side. Sends sound signal like a quail or a dolphin uses sound to determine distance," he said.
The location where the vessel sank Tuesday afternoon provided essential information that helped the San Francisco Police Department locate it.
In a statement Friday, SFPD said it "is working diligently with partner agencies and evaluating recovery options to determine whether it is safe and feasible to recover the wreckage of the Volare."
McMurdie described the recovery effort as one of the most challenging operations he has encountered.
"Every situation is unique. This has to be one of the most complex operations I have ever seen. One of the most complex I can imagine. The boat is very near if not within the shipping lane. So you've got large container shopman traffic going in and out all the time and there is a huge tidal current going in and out of the Golden Gate four times a day and you have a very short period of the slack tide when you are not affected by that current," he said.
The San Francisco Bay presents unique challenges for underwater recovery operations because of vessel traffic, strong tidal currents and limited periods of slack tide.
SFPD said investigators are continuing to examine what led to the incident and that efforts remain underway to recover the two missing passengers.
California Recovery Divers is a 100% volunteer organization. To donate to help with future rescue missions, click here.
Search ended at sundown Wednesday
Crews searched more than 814 square miles, according to the Coast Guard, and suspended their search "pending further developments."
Toczko previously said he would not dismiss the possibility that those missing could still be alive, though he also said some could have been trapped inside the three-deck, 49-foot cabin cruiser.
"We do know individuals were in the main deck and potentially below deck," he said. Witnesses described seeing people pounding on glass windows, trapped as the boat sank.
Why crews can't easily reach sunken SF Bay vessel
The search for the vessel continues as authorities work to locate the boat and assess how it can be recovered from deep water.
The focus has now shifted to locating the boat, identifying its condition underwater and determining how it can be raised.
Conditions in the Bay are making the effort increasingly difficult.
"It is at an extreme depth that divers cannot go past," said Brien Hoo, commander of the Special Operations Bureau.
Hoo said crews will need to evaluate the vessel once it is found.
"Once we located the boat, we have to send an underwater drone that will look at the feasibility and see how the boat is structurally sound and then we can look at the feasibility and working with our partners on raising the boat if needed," he said.
The San Francisco Police Department is now leading the recovery effort, confirming the vessel is at an estimated depth of 120 feet on a rocky seabed. The transition came after the Coast Guard completed an extensive search without locating the vessel.
Lt. Max Holloway of the U.S. Coast Guard said search efforts become increasingly complicated over time, particularly in the dynamic waters of the San Francisco Bay.
"Given the multiple tide cycles, the weather, the amount of vessels in the maritime transportation system I think just the dynamic of the San Francisco Bay and how large it creates such a dynamic search and recuse planning operation," Holloway said.
Authorities said the last time first responders saw the three-level vessel was Tuesday afternoon as it rapidly sank. Witnesses reported that three people were trapped inside and yelling for help.
As searches continue, officials said in incidents of this type the area that must be covered expands over time.
Asked how quickly a vessel can move underwater, Holloway said, "Underwater it can drift as fast as 3 knots we experience currents of that magnitude in the San Francisco however when something goes behind the water surface it's very difficult for our search assets to locate that."
Strong currents and shifting tides are expected to make recovery efforts even more challenging for divers.
"The tidal current through that area can be 5-6 knots so that's much faster than Michael Phelps swims as a point of reference and the tide changes directions twice a day and in between there a period if slack tide," said David McMurdie of California Recovery Divers. "The slack tide is maybe a half hour to an hour. It's a really short time so the amount of time you have to get your gear ready and get in the water got down in the water and check things out is really minimal."
Divers involved in similar recovery operations say underwater visibility is another obstacle. Once below the surface, conditions are often pitch dark, making technology critical for mapping the sea floor and helping determine where the boat may be located.
"You have about maybe 10 minutes of search time at the bottom maximum and 10 minutes of search when everything is blacked out and you can't see a hand in front of your face is nothing. 10 minutes to become oriented on a boat that is unstable on the bottom almost certainly damaged and has a lot of rigging and things like that going on. As a diver you are going into a situation that is like a fishing net waiting to capture you and kill you in the bottom of the bay," said McMurdie.
What led to the boat sinking?
Witnesses reported "rough seas," San Francisco Fire Department Chief Dean Crispen said, and rescuers said swells reached up to 5 feet. Marine weather conditions, however, didn't warrant a small craft advisory from the National Weather Service.
Fire department spokesperson Lt. Mariano Elias said the vessel, named Volare, was registered out of Stockton, California, which sits at the eastern edge of the Sacramento-San Joaquin River Delta.
According to the ship-tracking website VesselFinder, the boat departed a San Francisco marina, passed under the Golden Gate Bridge twice and visited Angel Island State Park, the largest natural island in the bay. It was on its way back to San Francisco when it sank near Alcatraz, the famous maximum-security federal prison which closed more than 60 years ago.
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Kirk Miller, an experienced local sailor with a master mariner license, said an uneven distribution of passengers could have caused the Volare to tip.
"As it rocks in the waves, it leans over a little bit," Miller said. "And as it leans over, the stability would decrease. If you had weight down below it acts as ballast. There was nothing in the conditions that were extreme in any regard. There was no massive gust of wind, no huge wave."
Like a 'Titanic' scene, rescuer says
Two men who jumped into action while fishing for halibut said the boat that sank was more than capable of being out in the bay. Justin Marceline and Michael Montoya said they saw what they thought was smoke and arrived to find the vessel halfway submerged.
"We just started yanking people out," Marceline told The Associated Press. At least two people bobbed in the water without life jackets, while others clung to a windsurfer's board.
Marceline could see people trapped inside the rapidly sinking boat through its windows. He threw lead fishing weights to survivors in the water, hoping they could smash the glass, but they were too weak.
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"It was like Titanic in real life," he said. "There was stuff everywhere. People were banging on the glass."
Montoya estimated they pulled eight or nine people aboard, including the captain, before first responders arrived.
Initial callers reported what appeared to be smoke coming from the boat, but San Francisco police officers who first reached the vessel said it was steam.
Toczko said there were life jackets on board the boat and that some people were rescued wearing them.
Sudden immersion in water under 60 degrees Fahrenheit can lead to cold water shock, a condition where people lose dexterity in minutes. That can be dangerous or deadly when trying to escape a sinking watercraft.
The owners of the boat are John Boisa and Miriam Boisa of Stockton, Coast Guard records show. They did not immediately respond to messages seeking comment.
Ralph Boisa said his brother John is a "very capable and experienced boatsman" who served in the U.S. Navy. He frequently took family members out on the boat to the San Francisco Bay, Boisa said.
His older brother who died, Clifford Boisa, lived on a small prune orchard in Sutter County in the Sacramento Valley and was a volunteer sheriff's deputy for more than a decade. Ralph Boisa had planned to visit him for his 80th birthday party next month.
"He was a happy guy, jovial," Boisa said. "We're pretty broken up here."
Stockton residents react to disaster in the Bay
Stockton neighbors and members of the Stockton Yacht Club are mourning the tragedy.
Noah Bonilla, who said he lives near the Boisa family, said he was shocked when he learned about the sinking.
"I found out yesterday, and it was super crazy. It was like, 'Woah, I can't believe this boat just sank,' and he was my neighbor," Bonilla said.
Bonilla expressed sympathy for those affected by the incident.
"You know it's horrible the death and I hope that everyone is recovery saftely mentally and physically and that they can move on from this," he said.
Outside the family's Stockton home on Wednesday, a printed note dated July 15 was posted on the front door.
"We and several families have suffered a horrific loss. We appreciate the outpouring of condolences and prayers. At this incredibly difficult time, we ask that you respect our privacy so that we can process this grief. Thank you," the note read.
The family did not speak publicly. A man who identified himself as the family's rabbi declined further comment while approaching the home.
The somber mood also extended to the Stockton Yacht Club, where members struggled to process the tragedy.
"I feel very sorry for his wife and his whole family of course. Excellent people. Love them. It's too bad for their hurt," yacht club member Christel Schnider said.
The Associated Press contributed to this story.
Stay with ABC7 News for the latest details on this developing story.