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2001 Chief of Naval Research Award of Merit for Group Achievement: MAI employees were honored by the Chief of Naval Research for Superior Group Effort while serving on the ONR LWAD Team. This citation credited the LWAD team with "...undertaking the task of developing a partnership with Commander SEVENTH Fleet units and forging a relationship with the Navy's Surface Warfare Development Group to optimize Fleet asset availability for at-sea S&T testing. This revolutionary approach fostered at-sea S&T exercises with far greater applicability to Littoral ASW and promoted more rapid transition of promising technologies to the Fleet." The award further commended the LWAD Team for "significantly contributing to the future of naval warfare, improving the performance of ... weapons systems, and dramatically enhancing the well-being of the ultimate recipient of our products—the Fleet warfighters."

U.S. Department of Justice Certificate of Commendation: On September 23, 2004, MAI received a Certificate of Commendation from the U.S. Department of Justice for "Outstanding Performance and Invaluable Assistance in Support of the Activities of the Environment and Natural Resources Division" signed by Tom Sansonetti, Assistant Attorney General.

The National Oceanographic and Atmospheric Administration's (NOAA) National Marine Fisheries Service (NMFS) convened a Review Panel from the Center of Independent Experts (CIE) to review MAI's Acoustic Integration Model© (AIM). Their December 2006 Summary Report concluded that: 1) The Panel agreed that AIM appears to be correctly implemented and that the animal movement appears to be appropriately modeled; 2) The Panel agreed that the principles of credible science had been addressed during the development of AIM and that AIM is a useful and credible tool for developing application models.This signifies that AIM is the only animal exposure model that has undergone an official peer review.

Captain Joseph P. Kelly Award: On October 19, 2007, Mr. George "Chuck" Gagnon of Marine Acoustics, Inc. was selected to receive the Captain Joseph P. Kelly Award. The award is given annually by Commander, Undersea Surveillance in recognition of innovation and ingenuity in the development or use of undersea surveillance system capabilities.

The award was established in 1992 and is named in honor of Captain Joseph P. Kelly, who, beginning in 1951, served as manager of Projects Jezebel and Caesar, leading the development and installation of the Navy's Sound Surveillance System (SOSUS).