A student from the Philadelphia College of Osteopathic Medicine riding a bicycle to Boathouse Row "saw what happened and immediately dived in," said Mayor Nutter, who spoke to the media after meeting with Naughton's family.
A third person arriving on the scene had a knife, which was finally used to cut Naughton free, Nutter said.
Naughton, who was reported by medics to be in cardiac arrest, was transported to Hahnemann University Hospital, where he was pronounced dead at 4:45 p.m.
Family members, including Naughton's wife and at least one of his two children, rushed to the hospital.
Nutter, Police Commissioner Charles H. Ramsey, and other top city officials and police commanders gathered at the hospital to offer their condolences and support.
The medical student was being treated Tuesday evening at Hahnemann for foot injuries. Police do not know the identity of the person with the knife.
"We're very proud of them and thank them profusely, and the family does as well," Nutter said of the Good Samaritans. He said the city would officially recognize them at a later date.
Shawn Duff, 25, an assistant rowing coach at St. Joseph's Preparatory School, was at a boathouse near the Strawberry Mansion Bridge when he was told about the accident and took a motorboat to the scene.
"There were three or four [people] in the river bobbing up and down," Duff said, describing the scene of rescuers repeatedly diving to reach Naughton.
Duff jumped in twice but said he was unable to grab hold of anything. Duff, who is 6 feet, 5 inches tall, said he was able to stand on the roof of the car with his head still above the water.
Naughton eventually was pulled from the water and secured to a harness to raise him over a river wall, Duff said. Naughton then was attached to a defibrillator and was given cardiopulmonary resuscitation before being taken away.
John McNesby, president of Lodge 5 of the Fraternal Order of Police, called Naughton "a pure gentleman."
Naughton helped coordinate police-merit ceremonies that are frequently held at the FOP's headquarters on Spring Garden Street near Broad.
"He never let anything slip by," McNesby said. "He always wanted to make sure the cops were recognized for everything they did.
"He also used to help us plan the details for funerals for our fallen officers. Now we're going to be planning his."
A steady stream of tearful relatives and friends shared their grief later in the evening at Naughton's home on Scotia Road.
Evelyn Bose, an 86-year-old widow who lives next door to Naughton's family, peered through her front window at parked police cruisers.
"This is too much of a shock," she said, as she wiped tears from her eyes.
Contact staff writer Robert Moran at 215-854-5983 or firstname.lastname@example.org.
Inquirer staff writer Mike Newall contributed to this article, which also contains information from staff reports.