The body was that of 15-year-old Gary Lynn Faulkner of the 70 block of Bolling Road in Portsmouth.
Crews were searching for the boy in Baines Creek near City Park on Thursday. His family told NewsChannel 3 that he has Asperger syndrome.
Emergency crews received initial reports about someone who had fallen into the water at around 2:10 p.m. on Thursday afternoon.
Police say the autopsy is still ongoing, as is the investigation. The case has been classified as a suspicious death and is being investigated by homicide detectives.