She departed New London with the coaling ship USS Camden on 4 December 1919 for Norfolk, Virginia and a winter deployment with the division in the Gulf of Mexico from 13 January to 27 March 1920.

After acting as a training ship at the Submarine School, New London for five months, she was ordered 6 May to Washington, DC, for air purification tests by the Naval Research Laboratory.

In 1932, R-3 conducted sound and radio experiments for the laboratory and trained personnel from the Deep Sea Diving School off Piney Point, Maryland.

R-3 was placed in reduced commission 26 April 1933 and after testing low-pressure valves for the Naval Research Laboratory, departed for Annapolis, Maryland, on 2 June 1933 where she served as a training ship for future generations of submariners.

She sailed 22 February 1934 for Guantanamo Bay and sound operations with Eagle 58, followed by training duty at Washington, DC, with the Deep Sea Diving School.