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Oxygen (O2) is a critical constraint on marine ecosystems. As oceanic O2 falls to hypoxic concentrations, habitability for aerobic organisms decreases rapidly. We show that the spatial extent of hypoxia is highly sensitive to small changes in the ocean’s O2 content, with maximum responses at suboxic concentrations where anaerobic metabolisms predominate. In model-based reconstructions of historical oxygen changes, the world’s largest suboxic zone, in the Pacific Ocean, varies in size by a factor of 2. This is attributable to climate-driven changes in the depth of the tropical and subtropical thermocline that have multiplicative effects on respiration rates in low-O2 water. The same mechanism yields even larger fluctuations in the rate of nitrogen removal by denitrification, creating a link between decadal climate oscillations and the nutrient limitation of marine photosynthesis.