Authorities say a woman walking on a trail by Frankford Creek noticed the body after 8 p.m. Sunday.
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She ran and flagged down a medic unit who then called police.
Specialized equipment was needed to be used to retrieve the victim's body, since the creek is about 30 feet below street level.
When investigators reached the location, they found shell casings, indicating the man had been shot at point-blank range and was not dumped there.
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Police believe the victim was in his 20s. They are still trying to identify him.
They say he had a gun in his waistband, but it was never removed during the shooting.
The search for a suspect continues.