The first PBM-1s entered service with Patrol Squadron Fifty-Five (VP-55) of the United States Navy on 1 September 1940. Prior to the outbreak of World War II, PBMs were used (together with PBYs) to carry out Neutrality Patrols in the Atlantic, including operations from Iceland. Following Japan's attack on Pearl Harbor, PBMs were used on anti-submarine patrols, sinking their first German U-boat, U-158 on 30 June 1942. PBMs were responsible, wholly or in part, for sinking a total of ten U-boats during World War II. PBMs were also heavily used in the Pacific War, operating from bases at Saipan, Okinawa, Iwo Jima and the South West Pacific.
The United States Coast Guard acquired 27 Martin PBM-3 aircraft during the first half of 1943. In late 1944, the service acquired 41 PBM-5 models and more were delivered in the latter half of 1945. Ten were still in service in 1955, although all were gone from the active Coast Guard inventory by 1958 (when the last example was released from CGAS San Diego and returned to the U.S. Navy). These flying boats became the backbone of the long-range aerial search and rescue efforts of the Coast Guard in the early post-war years until supplanted by the P5M Marlin and the HU-16 Albatross in the mid-1950s.
PBMs continued in service with the U.S. Navy following the end of World War II, flying long patrol missions during the Korean War. It continued in front line use until replaced by its direct development, the P5M Marlin, with the last USN squadron equipped with the PBM, Patrol Squadron Fifty (VP-50), retiring them in July 1956.
The British Royal Air Force acquired 32 Mariners, but they were not used operationally, with some returned to the United States Navy. A further 12 PBM-3Rs were transferred to the Royal Australian Air Force for transporting troops and cargo.
The Royal Netherlands Navy acquired 17 PBM-5A Mariners at the end of 1955 for service in Netherlands New Guinea. The PBM-5A was an amphibian with retractable landing gear. The engines were 2,100 hp (1,600 kW) Pratt & Whitney R-2800-34. After a series of crashes, the Dutch withdrew their remaining aircraft from use in December 1959.