Houston police said officers were called out at around 6:10 p.m. to the location.
Witnesses at the scene told authorities that two men were fishing along the bayou when one of them went into the water and never resurfaced.
HPD Commander Elizabeth Lorenzana said it is unknown if the man jumped into the water or if he lost his footing and fell in.
"It's very dangerous to go out into the bayou," Lorenzana said. "I recommend people not going to the bayou."
Officers described the victim as a Hispanic man in his 30s.
HPD units, a dive team, and the Coast Guard searched for the man.
The body was located around 10:30 p.m. Tuesday.