WEAU-TV reports the man's body was found Saturday afternoon. His name wasn't immediately released.
Assistant police Chief Jason Knecht says the man's body was found near the Golf and Country Club by a fisherman. An emergency helicopter flying overhead had also spotted something that looked like a body at about the same time.
Crews had been searching since Thursday night.
Police say two men were heading up the Eau Claire River when they got too close to the Altoona dam and flipped over. One of the men was able to swim to shore.