The Merced County Sheriff's Office was called out before 7 pm Thursday to the Cressey Bridge area on the river.
Witnesses told deputies that the man was struggling in the water and lost sight of him after being swept away by a current.
Dive equipment, a helicopter and drones were used in efforts to find the man.
Just before 11 pm Thursday, a diver found the man's body. He was declared dead at the scene.
Authorities are not releasing his identity at this time.