Searchers spotted the whales Tuesday morning still north of the bridge but moving downstream.
"The last report was they were headed in the right direction," California Department of Fish and Game marine biologist Carrie Wilson said.
Coast Guard crews and scientists planned to spend another day on the river banging metal pipes in the water in an effort to coax the whales back toward the Pacific. More than two dozen vessels were slated to join the whale herding operation, including an 87-foot Coast Guard cutter.
The humpbacks, nicknamed Delta and Dawn, had traveled 90 miles inland before turning around at the Port of Sacramento on Sunday. They were making progress Monday until they reached the Rio Vista Bridge and began swimming in circles.
Scientists theorized that the whales began circling because vibrations from traffic upset them. The pair could not be coaxed forward even when the drawbridge was raised to halt the flow of vehicles.
The U.S. Coast Guard tried positioning more than a dozen boats in front of them to turn them around, but the whales appeared unfazed.
Not so for their fans, who came out to see the rare sight of whales stuck in the middle of a farming community, reports CBS News correspondent Sandra Hughes.
"I'm not really sure where they're at — might as well bring the little man to come check it out," said a man who was carrying a toddler on his shoulders.
Scientists have been watching the two closely because their route includes sloughs leading to muddy deltas that could trap the whales, both already apparently wounded by a boat's propeller. The pair also face a couple more highway bridges between Rio Vista and San Francisco Bay.
Federal officials have authorized researchers to fire darts carrying a satellite tracking device beneath the mother's fin to monitor her location, but gusty winds and choppy waters Monday led scientists to postpone the tagging.
"They're at this point lost," Rod McInnis of the National Marine Fisheries Service.
"We believe they don't have any clue as to where the Golden Gate is," McInnis told CBS News.
It could take the whales a while to make it back to the ocean, reports Hughes. The last time a whale was stuck in the river, it took almost a month for it to find its way home.