Rescue teams were called to the River Taff at Upper Boat, Pontypridd, just after 06:00 BST on Thursday morning.
South Wales Fire and Rescue Service said the water was less than one metre (3ft) deep where the car was.
The man was taken to hospital but his injuries are unknown, as is the cause of the crash.
A motorist had to be rescued after his car ended up in the river in Rhondda Cynon Taff.