Over the next decade, the Fighting Marlins operated from detachment sites around the globe and participated in the prosecution of the newest generation of Soviet submarines. In 1991, VP-40 bolstered the U.S.-led effort to liberate Kuwait during Operation DESERT STORM. During this time, the squadron continued to add to its outstanding record of achievement, claiming three Arnold J. Isbell awards, the Coastal Command Trophy, and two Golden Wrench Awards. In 1993 and 1994, VP-40 won consecutive Battle Efficiency awards.
In 1993, Patrol Squadron FORTY left Moffett Field and moved up the coast to NAS Whidbey Island, the squadron's current homeport. The ensuing years marked several more changes for VP-40 and the Maritime Patrol community. During a WESTPAC deployment in 1997, the Fighting Marlins upheld their mantra of "Always Ready," proving adept at integrating new technology into their war-fighting arsenal. The squadron accepted the first AVX-1 electro-optical equipped CDU aircraft to be deployed to the SEVENTH Fleet, and they also participated in the first AGM-84E SLAM detachment to Qatar during a period of rising tensions between the United States and Iraq. From December 1998 to June 1999, VP-40 deployed to the Western Pacific and Persian Gulf in support of the FIFTH and SEVENTH Fleets under the operational control of CTF-72. Participation in Exercises TANDEM THRUST and COBRA GOLD, as well as several successful SAR missions, helped earn VP-40 the 1999 Battle Efficiency Award. During the ensuing Inter-Deployment Training Cycle, Patrol Squadron FORTY took part in the most successful prosecution of a Russian submarine since the end of the Cold War. Among seven participating squadrons, Marlin crews flew 230 hours and accounted for over half of the total contact time logged.