[8][9] Before Onondaga could be completed, she was transferred to U.S. Navy control because of the outbreak of the Spanish–American War on 24 March 1898 and the contractor was directed to cut the ship in half for transport to Ogdensburg, New York.

[2] On 8 December 1899, she received orders transferring her to Philadelphia, Pennsylvania, with a patrol area set from Great Egg Harbor to Fort Monroe, Virginia, including Delaware Bay.

While stationed at Philadelphia, she also had a temporary assignment escorting Marine Hospital Service ship Senator from Hampton Roads, Virginia, to Havana, Cuba, in June 1900.

[12] After 13 April 1907, all patrols were based out of Norfolk, with occasional temporary duty at Tompkinsville on Staten Island, New York, while the cutters normally stationed there were in shipyards for repairs.

[14] On 9 May 1913, Onondaga received United States Secretary of the Treasury William Gibbs McAdoo and his party aboard for a cruise from Baltimore, Maryland, to Richmond, Virginia.

[16] On 9 October 1913, the steel-hulled bark Manga Reva departed Philadelphia, Pennsylvania, bound for San Francisco, California, via Cape Horn with a cargo of coal, but about a week after she cleared Delaware Bay, her crew of 28 men mutinied while she was in the Atlantic Ocean 600 nautical miles (1,100 km) east of Bermuda.

The weather prevented the pilot who came aboard from guiding her up the Delaware Bay to Philadelphia, and as he disembarked Manga Reva′s captain, despite warnings from the mutineers not to mention the mutiny, slipped him a note asking for help.

With a small crowd of onlookers from Lewes using telescopes to observe the action from the beach, Onondaga arrived on the scene on 10 November 1913 and fastened herself to Manga Reva with grappling hooks.

[17][18][19] On 5 August 1914, at the outbreak of World War I in Europe, Onondaga was authorized for duty in enforcing neutrality laws in the Chesapeake Bay area.

[22] Onondaga arrived at Lewes and disembarked a detachment of 50 United States Marines carrying rifles with fixed bayonets, prompting the unarmed immigrants to return to the quarantine station.

With the approval of Onondaga′s commanding officer, Captain Benjamin M. Chiswell, they flew scouting missions in an airplane loaned to them by a representative of the Curtiss Aeroplane Company.

[27][28] On 20 February 1918, Onondaga rescued the entire crew of the British steamship SS Veturia after she foundered on Diamond Shoals off the North Carolina coast.

[29] While on patrol near Montauk Point on 13 March 1918, she came to the aid of SS Kershaw, taking some of the crew off the stricken ship and placing them aboard USRC Tuscarora.