Military operations may result in noise impacts on surrounding communities and wildlife. A recent transition to more powerful military aircraft and a national consolidation of training operations to Whidbey Island, WA, USA, provided a unique opportunity to measure and assess both in-air and underwater noise associated with military aircraft. In-air noise levels (110 ± 4 dB re 20 µPa rms and 107 ± 5 dBA) exceeded known thresholds of behavioral and physiological impacts for humans, as well as terrestrial birds and mammals. Importantly, we demonstrate that the number and cumulative duration of daily overflights exceed those in a majority of studies that have evaluated impacts of noise from military aircraft worldwide. Using a hydrophone deployed near one runway, we also detected sound signatures of aircraft at a depth of 30 m below the sea surface, with noise levels (134 ± 3 dB re 1 µPa rms) exceeding thresholds known to trigger behavioral changes in fish, seabirds, and marine mammals, including Endangered Southern Resident killer whales. Our study highlights challenges and problems in evaluating the implications of increased noise pollution from military operations, and knowledge gaps that should be prioritized with respect to understanding impacts on people and sensitive wildlife.