Officials say the first body was found when someone called 911 just before 2 p.m.
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The caller said they saw a body floating in the water near the Navy Yard along the 4500 block of South Broad Street.
Crews recovered the body of a man who was pronounced dead at the scene.
There is no word yet on his identity or what led to his death.
The second body was discovered in the city's Port Richmond section just before 5 p.m.
Philadelphia police and fire department crews say they responded to reports of a body in the water at East Allegheny Avenue in the Delaware River at General Pulaski Park.
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Officials located the body and the victim was pronounced dead a short time later.
Police have East Allegheny Avenue closed, blocking access to the park and riverfront.
There is no identification or cause of death listed for the second body.
Officials did not say whether the two deaths are related.