After offloading there, she went to Brisbane, Australia, to pick up the flight crews and aviation supplies, including spare parts and fuel, of Patrol Squadron 101 (VP-101), then returned to Nouméa to commence operations as tender and base for PBM Mariner and PBY Catalina flying boats conducting "Black Cat" night-fighting, air-search, and reconnaissance missions.

With VP-101 and assigned crash rescue boats, San Pablo formed Task Group 73.1 and established a seaplane base by charting the bay, setting out mooring and marker buoys, and constructing quarters for squadron personnel at nearby Honey Hollow.

For the next several months, the "Black Cats" operated from these bases, attacking on Japanese shipping along the coasts of New Guinea, New Britain, and New Ireland, and in the Bismarck Sea.

They inflicted great losses on Japanese inter-island barge traffic as well as to heavy shipping, harassed Japanese troops with night bombing and strafing missions; conducted photographic intelligence operations, provided at-sea search-and-rescue support for downed United States Army Air Forces fliers and sailors of sunken vessels, and carried high-ranking officers, Allied coast watchers, and native guerrilla units.

While continuously on the alert for enemy air attack, San Pablo sailors worked around the clock to fuel, repair, arm, and control the seaplanes and to feed and care for their crews.

On 9 October 1943, San Pablo was relieved at Nouméa by seaplane tender USS Half Moon and sailed to Brisbane for long-needed repair, replenishment, and shore leave.

Relieved by seaplane tender USS Orca on 26 May 1944, San Pablo then refueled PT boats at Humboldt Bay, New Guinea, and transported personnel and cargo between Manus Island, Seeadler Harbor, Emirau, and Mios Woendi.

In late December 1944, San Pablo joined Convoy "Uncle plus 15" en route to Mindoro and came under severe attack by suicide planes for three[1] consecutive days.

After attempting to aid the disabled Boeing 314 flying boat Honolulu Clipper 650 miles (1,050 km) east of Oahu[2] San Pablo arrived at Bremerton, Washington, on 17 November 1945 to prepare for inactivation.

On 3 February 1949, San Pablo departed in company with hydrographic survey ship USS Rehoboth (AVP-50), also a converted Barnegat-class seaplane tender, for oceanographic work in the western approaches to the Mediterranean Sea.

After a cruise to Casablanca, French Morocco, in July and August 1950, she returned to the United States East Coast to conduct survey operations between New London, Connecticut, and Key West, Florida, for the remainder of 1950.

From 1953 through 1968, San Pablo alternated between the North Atlantic and the Caribbean Sea, conducting studies on salinity, sound reflectivity, underwater photography techniques, deep-bottom core sampling, bottom profile mapping, and subsurface wave phenomena, as well as work on secret topics.

San Pablo was loaned for a time to the Ocean Sciences Center of the Atlantic in Savannah, Georgia, after which she was sold on 14 September 1971 to Mrs. Margo Zahardis of Vancouver, Washington.