The 36-foot pontoon flipped over near the Inner Harbor Saturday during a sudden storm with wind gusts up to 50 mph. Water temperatures were in the low 40s, and police did not expect to find any more survivors.
The missing victims were a man, a woman and a child, said Baltimore Fire Chief William Goodwin.
Search crews used sonar equipment and dogs trained to find bodies submerged in water early Sunday as they resumed a full search. Goodwin said the dogs may have detected something near where the boat sank, and searchers planned to check that area again before sending in divers.
Goodwin said the storm caught the boat as it set off to cross the harbor from Fort McHenry to Fells Point. The boat, which was at full capacity, was equipped with life preservers, but passengers are not required to wear them.
"No one on the craft had time to get their life preservers on," said Maj. Frederick Bealfeld of the Baltimore Police Department.
Rescuers said they saw up to a dozen people climbing across the bottom of the craft after it flipped.
"It was like the twilight zone. It was eerie how the weather just overtook the vessel," said Command Master Chief Melvin Johnson, who was among a group of Naval reservists training nearby when the boat overturned.
Ellen Engleman-Conners, chairwoman of the National Transportation Safety Board, said the accident recalled the October 2003 crash of a Staten Island ferry that killed 10 people when it slammed into a pier.
"This is unfortunately all too similar to the issue with Staten Island, in which once again we have passengers that are crossing in essentially a small ferry," Engleman-Conners said.
She said she was concerned about a trend relating to "passenger safety when we're crossing the water. ... It's something we're definitely reviewing."
Engleman-Conners said investigators were focusing on interviewing witnesses and passengers. Capt. Francis Deppner, the boat's captain, was among those who talked with investigators, said Tracey Weinberg, a spokeswoman for the Living Classrooms Foundation, which operated the water taxi.
Petty Officer Edward Mendez said he watched wind gusts toss the vessel "like a little toy boat getting blown out of control."
Johnson said reservists immediately began throwing on life jackets and raced to boats to help.
By the time they reached the pontoon, it had been blown about two miles into the Patapsco River near the marine terminal in Dundalk, Goodwin said.
Once reservists got close enough they lashed their own boat to the overturned craft and began pulling people to safety, he said.
Twenty-two people were removed from the water, including one woman who died at a hospital. Seven remained hospitalized Sunday afternoon.
Police declined to identify any of the passengers, saying that 18 of the 25 people on board were from out of town and they wanted to give people a chance to tell their relatives what happened.
Maj. Fred Bealefeld of the Baltimore Police Department said three of the people on board were from Puerto Rico. He said others were from Illinois, New Jersey, North Carolina and Virginia.
Of the 25 on board, 23 were passengers and two were crew members. Both crew members survived.
The agencies scaled back their search before midnight and stopped helicopter searches about 1:30 a.m. Sunday, Goodwin said. They resumed early Sunday.
Goodwin remarked on the coincidence that the reservists happened to see the accident.
"Had no one been looking, this tragedy would have been far more tragic than it was," he said.
"It's fortunate there was not a greater loss of life when you consider the force of the storm," said Baltimore Mayor Martin O'Malley.
The Inner Harbor is one of the nation's oldest seaports, visited by millions of tourists each year who walk along brick promenades on the shore and frequent the many shops, seafood restaurants, museums and other attractions.
Among the attractions are Fells Point, the world-renowned National Aquarium and Fort McHenry, best known for hoisting the flag that inspired the poem by Francis Scott Key that became the national anthem.
The boat was part of a fleet of 11 Seaport Taxis operated by the Living Classroom Foundation.
"She was ready for an inspection on Monday and in shape the way she should be," said the organization's president, James Bond.
Bond said in deference to the families of the victims, the company would not operate taxis on Sunday. The taxis transport about 250,000 people, mostly tourists, every year.