USS Seneca has been the name of more than one United States Navy ship, and may refer to:
USS Seneca (1861), a gunboat in commission from 1861 to 1865
USS Seneca, the pre-commissioning name of the steamer USS Currituck (1861), in commission from 1862 to 1865
USS Seneca (SP-427), a minesweeper and patrol vessel in commission from 1917 to 1919
USS Seneca (SP-1240), a barge in commission from 1917 to 1919
USS Seneca (SP-1824), the originally planned name and designation of a cargo ship commissioned as USS Wabash (ID-1824) and in commission from 1918 to 1919
USS Seneca (AT-91), a tug in commission from 1943 to 1971
