Authorities received a 9-1-1 call from a woman shortly after 12 noon. She and another passenger overturned their canoe on the river near Lost Lake Park.
The women say they had been riding in their canoe for about 10 minutes when they hit some low lying tree branches.
As their boat overturned, they were able to grab on to the limbs and one of the women used her cell phone to call for help.
Rescuers had a hard time finding the women because they were hidden in the trees.
Chris Curtice with the Fresno County Sheriff Dept. said, "There is so much water down here. It just has made a completely different river. There are a lot of little tributaries if you will. There are trees and branches hidden just below the surface. A lot of islands out there."
Emergency teams were finally able to locate and rescue them. Both were taken to the hospital and treated for mild hypothermia.