Throughout the ocean, countless small animals swim to depth in the daytime, presumably to seek refuge from large predators^1, 2. These animals return to the surface at night to feed^1, 2. This substantial diel vertical migration can result in the transfer of significant amounts of carbon and nutrients from the surface to depth^{3, 4, 5, 6, 7}. However, its consequences on ocean chemistry at the global scale have remained uncertain^8, 9. Here, we determine the depths of these diel migrations in the global ocean using a global array of backscatter data from acoustic Doppler current profilers, collected between 1990 and 2011. We show that the depth of diel migration follows coherent large-scale patterns. We find that migration depth is greater where subsurface oxygen concentrations are high, such that seawater oxygen concentration is the best single predictor of migration depth at the global scale. In oxygen minimum zone areas, migratory animals generally descend as far as the upper margins of the low-oxygen waters. Using an ocean biogeochemical model coupled to a general circulation model, we show that by focusing oxygen consumption in poorly ventilated regions of the upper ocean, diel vertical migration intensifies oxygen depletion in the upper margin of oxygen minimum zones. We suggest that future changes in the extent of oxygen minimum zones could alter the migratory depths of marine organisms, with consequences for marine biogeochemistry, food webs and fisheries.