The Admiral praised Waterman's "through planning, attention to detail, and exceptional ability" that indicated a "high degree of efficiency" instrumental in the success of that important mission.
Transferred to VP-1 in September 1940, PatWing 10 flew reconnaissance and patrol missions from Cavite's Sangley Point seaplane base or from tender-supported Olongapo up to the outbreak of war with Japan on 8 December 1941.
Before midnight on 26 December 1941, a six-plane attack group of PBY's from VP-101 (the redesignated VP-1) departed their advance base at Ambon, Netherlands East Indies, and set course for the Philippines.
In the ensuing running fight the fighter's cannon shells tore into the plane's gasoline tank; and the volatile fuel spilled from the ruptured area.
Waterman departed Pearl Harbor on 6 March and screened the escort carrier Nassau (CVE-16) as she ferried replacement aircraft, passengers, and cargo to Kwajalein, Majuro, Tarawa, and Makin in the Marshalls and Gilberts.
Underway again from Eniwetok on 26 July, Waterman rendezvoused with the fleet service group east of the Marianas and protected the oilers as they refueled the ships supporting the landings on Guam.
Waterman – operating out of Manus through September – weighed anchor on 4 October and stood out to sea, escorting the fleet service group to points east of the Philippines, where they replenished carriers launching air strikes smashing Japanese positions on the island of Leyte.
Winds of 120 knots (220 km/h; 140 mph) threw almost solid clouds of spume and spray and whipped up waves of about 80 feet in height, making life aboard Waterman decidedly "uncomfortable."
She spent much of January supporting the occupation of Luzon from the fueling areas east of the Philippines and, in February, escorted the vital auxiliaries to a rendezvous with the fleet that soon commenced the pre-invasion bombardment of Iwo Jima.
The destroyer escort's repair parties, operating under extremely hazardous conditions, streamed thousands of gallons of water on Patuxent's blaze and finally extinguished it.
During the first two weeks of April, Waterman escorted Attu (CVE-102) as she ferried replacement planes to the fast carrier task forces on two round trips between Okinawa and Guam.
On 21 August, less than a week after Japan capitulated, Waterman was assigned to TG 35.80, a special support group set up to enter Tokyo Bay as part of the initial occupation force.
With their "battle colors" flying, she and Kyne (DE-744) – the first destroyer escorts to reach Sagami Wan – entered that body of water just southwest of the erstwhile enemy's capital city of Tokyo on 28 August and dropped anchor less than a mile off shore from the town of Katase.
On 31 August, she moved into Tokyo Bay proper and, two days later, hauled down her "battle flag" as surrender terms were signed on board the battleship USS Missouri.
Waterman continued that work of mercy until 10 September, when she departed the Tokyo area with TU 30.6.3—four LSM's and sister ship Weaver (DE-741) – bound for Shiogama, on the eastern coast of Honshū, through which port the POW's from the Sendai camp were being evacuated.
On the afternoon of 29 September, Waterman received homeward-bound orders after 20 months of duty in the Pacific war zone; and she stood out of Tokyo Bay on 2 October.
After steaming via Pearl Harbor, she arrived at San Pedro, California, on 20 October and remained there until 6 November, when she got underway for the Panama Canal Zone and Philadelphia, Pennsylvania.