Keith Tolbert, 34, and two alleged prostitutes, Angel Weston, 21, and Stephenie Foulke, 22, face murder charges, The Philadelphia Inquirer reported.
A fisherman found Francis Zarzycki's body Tuesday in the river. Investigators believe he was killed Aug. 26 in a robbery attempt and that Tolbert then used an ax to dismember the body and wrapped it in plastic before dumping it.
The head, arms and legs had not been found. The body was identified by tattoos.
Zarzycki's family in Northeast Philadelphia reported him missing last week.
Sources told the Inquirer Zarzycki's father, a retired police officer, discovered an address in the Gray's Ferry neighborhood on his son's computer and found his car parked near there, leading police to the three suspects.
Capt. James Clark, a commander in the Philadelphia homicide unit, described Zarzycki, 40, as a frequent visitor to the apartment where Tolbert allegedly ran a prostitution operation.