The oceanographic conditions of the Southern California Bight (SCB) dictate the distribution and abundance of prey resources and therefore the presence of mobile predators, such as Cuvier’s beaked whales (Ziphius cavirostris). Cuvier’s beaked whales are deep-diving odontocetes that spend a majority of their time foraging at depth. Due to their cryptic behavior, little is known about how they respond to seasonal and interannual changes in their environment. This study utilizes passive acoustic data recorded from two sites within the SCB to explore the oceanographic conditions that Cuvier’s beaked whales appear to favor. Utilizing optimum multiparameter analysis, modeled temperature and salinity data are used to identify and quantify these source waters: Pacific Subarctic Upper Water (PSUW), Pacific Equatorial Water (PEW), and Eastern North Pacific Central Water (ENPCW). The interannual and seasonal variability in Cuvier’s beaked whale presence was related to the variability in El Niño Southern Oscillation events and the fraction and vertical distribution of the three source waters. Cuvier’s beaked whale acoustic presence was highest during the winter and spring and decreased during the late summer and early fall. These seasonal increases occurred at times of increased fractions of PEW in the California Undercurrent and decreased fractions of ENPCW in surface waters. Interannual increases in Cuvier’s beaked whale presence occurred during El Niño events. These results establish a baseline understanding of the oceanographic characteristics that correlate with Cuvier’s beaked whale presence in the SCB. Furthering our knowledge of this elusive species is key to understanding how anthropogenic activities impact Cuvier’s beaked whales.