USS Seneca was a Unadilla-class gunboat built on behalf of the United States Navy for service during the American Civil War.

One of the "Ninety-day gunboats", Seneca – the first United States Navy ship to be so named – was built at New York City by Jeremiah Simonson and launched on 27 August 1861.

On 5 November 1861, Seneca and three other Federal Union gunboats engaged and dispersed a Confederate squadron near Port Royal, South Carolina; two days later, she took part in the capture of Port Royal, which proved to be an invaluable Union naval base throughout the remainder of the Civil War.

On 28 February, in the Ogeechee River, she supported USS Montauk in the destruction of privateer Rattlesnake, the former Confederate warship CSS Nashville.

One of her crewmen, Chief Boatswain's Mate Othniel Tripp, was awarded the Medal of Honor for his actions in that battle.