The humpback mother and her calf started moving southwest on the Sacramento River at around 3:30 p.m. and were about five miles outside the Port of Sacramento late Sunday afternoon, Coast Guard Petty Officer Brian Leshak said.
"Nothing triggered it. They just started moving on their own," Leshak said.
The wayward pair were being followed by nine vessels carrying Coast Guard officers and wildlife officials to make sure they did not reverse course.
The whales still have a long way to go and obstacles to overcome if they maintain their course. Officials say there are sloughs leading to muddy deltas that could trap the injured whales, which appear to have been wounded by a ship's propeller.
The whales will also have to make their way through the pylons of four bridges to reach the San Francisco Bay, and will have to swim under the Golden Gate Bridge to return to the ocean.