After a frantic rescue effort, 35 people were plucked from the water, but two passengers remained missing late Wednesday - a 16-year-old girl and a 20-year-old man, both tourists from Hungary.
"We are actively searching for the two unaccounted-for individuals," Mayor Nutter said from the riverfront. "We are putting all of our effort and forces into that on the water, in the air."
The search was called off late Wednesday night and will resume Thursday morning. A Coast Guard ship was stationed near the site of the wreck.
The sunken vehicle was found at a depth of 40 feet using sonar, and police divers entered the murky water about 5:30 p.m., three hours after the accident. The divers could not tell if the missing passengers were still inside.
"You can't see three inches in front of you," said Philadelphia Police Commissioner Charles H. Ramsey.
The amphibious tourist vehicle - operated by Ride the Ducks - launched just south of the Benjamin Franklin Bridge before mechanical difficulties and a fire forced it to shut down, said Lt. Frank Vanore, a police spokesman.
"The boat was sitting on the water waiting for help," he said.
A city-owned barge, being pushed upriver by a private tug company, hit it.
The National Transportation Safety Board and the Coast Guard were investigating, authorities said.
The barge, the Resource, hauls sludge from the city's Northeast Wastewater Treatment Plant to the recently privatized sludge plant in Southwest Philadelphia run by Philadelphia Biosolids Services.
The barge, which is unmanned and unmotored, was empty. The city has a contract with K-Sea Transportation Partner L.L.C., which operates the tugboat that was pushing the barge.