Images from a remotely-controlled miniature submarine showed the Independence sitting on the ocean floor about 50km off the coast near the Farallon Islands.
The Independence operated in the Pacific during the war and served as a target ship for two Bikini Atoll atomic bomb tests in 1946.
Despite the damage suffered from the blasts, the Independence continued to float. The Navy used her to study nuclear decontamination.
The Independence was scuttled in 1951 out of concern the damaged ship would sink near the city.
The contamination poses little danger to public health because of the ship's isolation 800 meters underwater and far from the coast, scientists say.
"The risk to the public now is extremely small. Water is a very efficient shield," Kai Vetter, a University of California, Berkeley, nuclear engineering professor, said.
