Snapper fitted out at the Boston Navy Yard, then began three years of training and tests along the East Coast and in Chesapeake Bay.

She joined in Fleet maneuvers helping to develop submarine tactics in submerged attacks on combatant ships, and engaged in operations with airplanes in the infancy of naval aviation.

Highlights of the period were the reviews of the Fleet by President of the United States William H. Taft and Secretary of the Navy George von L. Meyer in November 1911 and October 1912.

Five days later the ships completed the 700 mi (1,100 km) passage, at that time the longest cruise made by United States submarines under their own power.

C-5 operated in Panamanian waters, conducting exercises and harbor defense patrols as well as studying the suitability of various ports of Panama for submarine bases.