Mid-frequency (< 10 kHz) acoustic sonar, used in naval training exercises, is known to adversely affect sensitive marine mammals. Less is known about the effects of higher frequency sonar sources (>10 kHz)  such as multibeam echosounders—on marine mammals. To date, no controlled studies have been conducted to evaluate the effect of multibeam echosounders (MBES) on marine mammals in the wild, despite the widespread use of this sound source in scientific research and geophysical work. Here the temporal and spatial effect of deep-water MBES signals on Cuvier’s beaked whale foraging behavior was assessed during two deep-water MBES ocean mapping surveys of the Southern California Antisubmarine Warfare Range (SOAR). The SOAR contains an array of 89 hydrophones spanning an 1800 km2 area that was used to detect echolocation clicks from foraging beaked whales during the mapping surveys. The acoustic data from the array was also used to assess and characterize the change in sound levels of the marine acoustic environment during one of the MBES ocean mapping surveys.