Police say the body was found a few miles away from Levi's Stadium, but have not confirmed it is that of 32-year-old Ian Powers.
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Powers vanished after Monday night's Giants-49ers game.
His girlfriend says the Army vet left his seat to use the bathroom, then never returned.
Police and family have been searching day and night since he vanished.
Fishermen made the gruesome discovery near the Alviso Marina Saturday afternoon.
"I was told it was about a mile out from the boat ramp," officials said.
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The coroners office is working to identify the body.
Authorities say it is possible he walked into a marsh near the stadium. They are also not ruling out foul play or a medical problem.
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