The boat, which was at full capacity, was equipped with life preservers but passengers are not required to wear them.
Investigators, whose work has already begun, are already looking at one possible factor in the accident: the timing of the government's bad weather warnings.
The Baltimore Sun reports that the National Weather Service's warning telling boats to get off the water did not come until four minutes after the first 911 call reporting that the water taxi had capsized.
"Perhaps the special marine warning should have been issued earlier, but I wasn't sitting at the radar screen," Andy Woodcock, a National Weather Service forecaster, told the Sun, saying that the NWS will try to determine whether an emergency warning could have been issued sooner. "I know our people were working very hard."
A group of Navy reservists who happened to be nearby are being hailed as heroes for their quick work in saving 21 of the passengers and crew who were aboard the vessel when it flipped.
Survivors - clinging to the overturned vessel in frigid, choppy water pounded by rain - told rescuers as they arrived that other passengers were trapped below.
A 60-year-old woman was killed in the accident in Baltimore Harbor and three people, including a 6-year-old boy, are missing.
Reservists talking about the accident Sunday said they were relieved the loss of life wasn't even greater.
The sailors rushed to the scene after seeing the boat in trouble. After passengers clinging to the water taxi told them others were trapped underneath, the rescuers used a ramp on their troop landing ship to lift the water taxi partly out of the water, Petty Officer Jeffrey King said.
"Brother, it was like the end of the "Titanic" movie once that thing lifted up," King said. "I mean those bodies just floated up."
Lt. Cmdr. Art Eisenstein said he jumped into the water and grabbed a little girl who was unconscious and floating face down.
"Just to hear that she's still with us is just amazing," Eisenstein said.
Water temperatures were in the low 40s, and heavy rain was pouring from black clouds as survivors were pulled out of the water.
"It was pretty hateful," Petty Officer Henry Zecher said. "I'm relieved that we were able to save as many lives as we were."
Fire and police officials also assisted in the rescue.
"The rescue efforts that happened yesterday were nothing short of miraculous," Baltimore Fire Chief William Goodwin said. "They were able to pluck people out of the water almost immediately."
Two people, an 8-year-old girl and a 30-year-old woman, were critically injured when the 36-foot pontoon boat overturned with 23 passengers and two crew members.
The ferry had just set off across the harbor from historic Fort McHenry on the way to the city's Fells Point when it was caught by wind gusting to 50 miles per hour.
Twenty-two people were removed from the water but one woman died at a hospital. Seven remained hospitalized Sunday. The water temperature was in the low 40s.
On Sunday, recovery crews used boats, helicopters, sonar and dogs trained to find submerged bodies in the search for the boy, a 26-year-old man and 26-year-old woman. They stopped about 6 p.m. because of bad weather, and officials said they would begin again early Monday morning.
Authorities had not released the victims' names by Sunday evening.
The missing boy was identified as Daniel Bentrem by Thomas Tran, a college student living with the boy's parents, George and Elizabeth Bentrem of Rockingham County, Va.
Tran told The Daily News Record of Harrisonburg that Daniel's 8-year-old sister, Sarah, was admitted to the University of Maryland Medical Center and has been released from the trauma unit.
George and Elizabeth Bentrem and another daughter, 7-year-old Katie Bentrem, were pulled from the water and uninjured, Tran said.
Investigators said they are looking at the weather and the condition and operation of the vessel as possible factors in the accident.
National Transportation Safety Board Chairman Ellen Engleman-Conners said officials have been interviewing survivors and witnesses, and are awaiting the results of voluntary toxicology tests conducted Sunday on the captain and first mate.
Engleman-Conners said the boat will be removed from the water so investigators could do complete hull and steering system inspections. She said an initial inspection found that the steering system appeared to be intact.
She said officials also inspected five other boats operated by the Living Classrooms Foundation, which operates the 11 Seaport Taxis.
A spokeswoman for the nonprofit group said the boat's captain, Frank O. Deppner, has talked to investigators.
The foundation's president, James Bond, said the boat "was ready for an inspection on Monday and in shape the way she should be."
Deppner released a statement Sunday night saying he "was deeply saddened by the tragedy."
Deppner said the NTSB asked him not to comment on specifics but he added, "I would like to extend my sincere concern and condolences to the passengers and families."
Police Maj. Fred Bealefeld said three of the people on board were from Puerto Rico and others were from Illinois, New Jersey, North Carolina and Virginia.
Engleman-Conners said she saw similarities to the October accident in which a Staten Island ferry slammed into a pier after crossing New York Harbor, killing 10 people.
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."
NTSB investigator Bill Woody said the accident also was similar to the 1984 sinking of a paddlewheel excursion boat in the Tennessee River at Huntsville, Ala., that killed 11 people. The Coast Guard said that accident was caused by a severe thunderstorm.