F-3 completed her trials in the Puget Sound area before reporting for duty at San Francisco, California, on 15 October 1912, when she joined the First Submarine Group, Pacific Torpedo Flotilla.

The Flotilla operated along the coast of California, conducting constant exercises and experiments to develop the techniques of submarine warfare, and from August 1914 to November 1915, carried out similar operations in the Hawaiian Islands out of Naval Submarine Base Pearl Harbor.

She engaged in daily operations, surfaced and submerged, training students of the submarine school.

F-3 suffered a cracked bow cap and after repairs at Mare Island Navy Yard was assigned operations in cooperation with a civilian motion picture company in experiments with underwater photography.

This article incorporates text from the public domain Dictionary of American Naval Fighting Ships.