Witnesses said they saw the boy fall into the river and his father jumped in to save him.
The Riverside County Fire Department said it received a call Monday afternoon about a possible drowning in the river in the Whitewater Canyon area, north of Palm Springs.
Rescue crews found the man's body about two hours later. His 10-year-old son was taken to a hospital in critical condition.
No other people were missing, Riverside County sheriff's officials said.
City News Service contributed to this report.