Thirty-five passengers survived with minor injuries and were recovered by police, fire, and Coast Guard vessels.
The crash, at 2:39 p.m., occurred off Columbus Boulevard near Chestnut Street. A Coast Guard Lt. Commander said there was no record of a distress call from the duck boat.
Police Commissioner Charles H. Ramsey said the divers' search for the two missing passengers was impeded by the murky waters.
"They don't know if the bodies are inside the boat because so dark," said Ramsey. ""You can't see three inches in front of you."
Ramsey added that they would bring the boat up and search it, but he did not know how long that would take.
The duck boat - operated by Ride the Ducks - launched just south of the Benjamin Franklin Bridge and encountered mechanical difficulties and a fire that forced it to shut down, said Police Department spokesman Lt. Frank Vanore.
"The boat was sitting on the water waiting for help," Vanore said.
The National Transportation Safety Board will investigate the accident, Vanore said.
The 250-foot barge, named the Resource, was being pushed by a tug on its port side.
Witness Talmadge Robinson saw the duck boat stopped in the river. A nurse's assistant, Robinson said he was sitting ashore when he saw the barge approaching the immobile vehicle. "There was a really loud bang. The thing was a sitting duck." Robinson said he helped pull three children in life jackets out of the water.
He and others ashore grabbed emergency fire hoses and ropes lying on the dock and threw them towards the survivors. "People were screaming."
Robinson, from Philadelphia, said it appeared the tug had enough time to avoid the duck boat.
"I looked out and all of these kids were in the river." He said there were "a lot of kids."
"They were pretty scared. All they could say was 'thank you.' " said Robinson, who was still dressed in blue medical scrubs from his job.
Robinson said when uniformed police arrived they dived into the water to rescue the children. He said it took about 10 minutes for the children to slowly drift to within reach.
Other children were swimming toward the Camden side. They were not wearing life jackets, and were rescued by police.
Passengers on commercial vessels do not have to wear life jackets, according Chris Edmonston, director of boating safety at the Boat US Foundation.
Norman Civera, 41, said he witnessed the barge hit the duck boat.
"It hit pretty hard and pulled the boat under," Civera said. "It went straight under."
He saw passengers getting rescued from the water, he said. Some were screaming.
A large group of the duck boat tourists were from Hungary, including three children who were transported to Hahnemann University Hospital, a medic said.
Harry Burkhardt, a merchant marine captain who volunteers on the USS Olympia, got a brief description of what happened from his 18-year-old son Kyle Burhardt, a deckhand on the ill-fated duck boat.
"He called me after it happened to let me know he was safe," said Burkhardt, 53, of South Philadelphia. "My son was on that boat working as a deckhand!
"He said the barge ran over the duck boat and it sank," he said. "Everybody went into the water."
Burkhardt said his son and others were taken to the Independence Seaport Museum to give statements about what happened.
"They thought might have gotten everybody out of the water but they weren't sure," he said.
Burkhardt is president of the Friends of the Cruiser Olympia, a nonprofit which is trying to raise money for the preservation of the ship.
Witness Jason Tilghman said the duck boat had stopped in the river for about 5 to 10 minutes. A crew member screamed "jump!" to the passengers and jumped in himself. Four passengers leaped in after him before the barge crashed into the back of the duck boat, pushing it 150 feet north toward the Benjamin Franklin Bridge.
Tilghman said the duck boat became dislodged and capsized.
Senes Deleon, 60, saw the collision from the Camden waterfront.
"I don't know how the guy driving the big boat no see the little boat," Deleon said.
The Captain of the Port of Philadelphia closed the river to all traffic between the Walt Whitman and Ben Franklin bridges until further notice.
Tourists board the duck boats, a popular tourist attraction, at Independence Mall. After touring Old City, the boats enter the river for a brief tour at a ramp just south of the Ben Franklin Bridge.
Ride the Ducks, which began operating in Philadelphia in 2003, runs 15 duck boats in the city. It launches its vessels from a ramp it built on property owned by the former Penn's Landing Corp.
Ride the Ducks is currently owned by the Herschend Family Entertainment company, which is located near Atlanta and operates Camden's Adventure Aquarium, the Dollywood theme park, as well as many water and adventure parks.
The company was founded in 1977, and operates about 90 vessels in several cities, including Atlanta, Baltimore, Memphis, Tenn., and Branson, Mo. It began its Philadelphia tours in 2003, using World War II-era DUKW landing craft.
According to the company's website, the vehicles used in Philadelphia are "based on the classic WWII DUKW amphibious design. Today, we build our vehicles from the ground up using the latest in marine design and safety."
It added the vehicles are "regularly inspected, tested & certified by the United States Coast Guard."
Duck boats have been involved in previous fatal accidents.
In June 2002, four people were killed in Ontario when the Lady Duck sank in the Ottawa River near Canada's Parliament.
In a 1999 accident, the Miss Majestic, sank and killed 13 passengers in Hot Springs, Arkansas.
Ride the Ducks reported to the National Transportation Safety Board 11 accidents in 2006, 12 in 2007 and nine in 2008 – all of them minor, traffic-related incidents, such as fender-benders. None of the incidents happened on the water, and no injuries appear to have resulted. Figures for 2009 were not available.
The Inquirer will post more details as they become available.
Contact staff writer Sam Wood at 215-854-2443 or email@example.com.
Inquirer staff writers Robert Moran, Miriam Hill, David O'Reilly, Kia Gregory, Marcia Gelbart, Edward Colimore, Jan Hefler, Darran Simon, Troy Graham, Joseph A. Gambardello, and Matt Flegenheimer contributed to this article.