The Navy said in a statement that about 2,000 gallons of oily waste spilled into the scenic waterway during a transfer of ship overboard discharge Monday afternoon.
The spill initially was estimated to be about 150 gallons.
The Navy, the state Department of Ecology and the U.S. Coast Guard are working together to contain and clean up the spill, which was caused by a malfunction in a pierside oily waste transfer system at the base.
Containment booms were placed around the spill, but not before an unknown quantity of oily waste escaped.
Oil spill response equipment from several regional Navy commands is on scene supporting the cleanup.
The effects of this spill to wildlife or property are unknown at this time, said Navy spokesman Tom Danaher.