Anthropogenic noise is increasingly recognized as a potentially significant stressor for marine animals. Beaked whales, deep-diving cephalopod predators, have been disproportionally present in atypical mass stranding events coincident with military sonar exercises, while frequently disturbed populations that do not strand may have reductions in fitness. We present in situ measures of prey availability, a key factor affecting fitness, for 2 distinct populations of Mesoplodon densirostris: one on a US Navy range in The Bahamas and one nearby in an area less exposed to sonar. The variables most strongly correlated with beaked whale habitat use were related to the distribution of deep-sea squid (mode spacing, peak depth, and 100 m scale variability). All squid metrics were more favorable for beaked whales at the less exposed site than those on the range. To develop a generalized functional relationship between prey resources and beaked whale habitat use, data from The Bahamas were combined with comparable data from another Navy range and the larger beaked whale, Ziphius cavirostris. A power-law relationship was observed between a normalized metric of prey quality and whale habitat use. A critical threshold in prey characteristics, below which beaked whales appear unlikely to be successful, but above which small changes in resource availability enable large gains for predators, was observed. This implies that modest changes in the behavior of individual whales associated with disturbance can have consequential population effects. Our results elucidate the ecological realities of these elusive and sensitive beaked whales, and the importance of environmental context in effective spatial planning for the deep sea.