Bigeye tuna are targeted by longliners and caught incidentally by purse seiners in the tropical Pacific. The spawning biomass has been reduced significantly from unexploited levels, necessitating management action in both the western and central Pacific and eastern Pacific. Stock assessments of bigeye tuna rely primarily on data from the fisheries; however, the vulnerability of the stock to these gears, and its spatiotemporal variability, remains poorly understood, requiring simplifying assumptions to be made in the stock assessments. We analyzed the vertical behavior of 65 bigeye tuna (estimated size range 48–130 cm fork length) tracked with archival tags in the equatorial Pacific Ocean and the Coral Sea, and found that fish depth shows a clear gradient with longitude, becoming progressively shallower from west to east. Additive mixed models were used to explore potential relationships of the depth behavior during both day and night to several life history and environmental variables. Swimming depths were most clearly related to the thermocline depth, the intensity of temperature stratification of the water column and fish size. The model predictions suggest strong relationships between fish depth and fisheries catch-per-unit-effort (CPUE) both spatially and temporally. In particular, we propose that El Niño-Southern Oscillation-driven changes in oceanography have a major influence on fish depth and longline CPUE, which could have substantial implications for stock assessments where longline CPUE is used as an index of abundance.