Shallow coastal deoxygenation is poorly documented in the tropics. Despite concurrent warming, little is known about how hypoxia and warming impact reef associated taxa. On the three different reef habitats in the Caribbean (CAR) and Equatorial Pacific (TEP) we measured oxygen and temperature, and used these measurements to calculate the amount of oxygen available for biological use over the last three years. The first site is a protected reef within a large bay, while the second site is nearby on a well-exposed reef facing the open ocean in the CAR. The third site is also well-exposed ocean facing, but is in the TEP and experiences upwelling. Seasonal hypoxia is prevalent each of these reef habitats, with cold-correlated hypoxia in the TEP and warm-correlated hypoxia in the CAR. Using Echinometra sea urchin sister species from both oceans, we relate the most severe conditions measured at these sites to their modern-day physiological capacity to both perform under and survive the conditions on the reefs they inhabit. The TEP Echinometra performs poorly after only two hours in hypoxia, and is unable to survive hypoxia when temperatures increase despite O₂ availability increasing with temperature. Conversely, the two CAR Echinometra species are better equipped to survive short bouts of hypoxia, even when coupled with high temperatures. However, performance trials suggest only one of Caribbean species is able to cope reasonably well with the most extreme conditions documented on the reefs. Results suggest that tropical marine biodiversity is at greater risk than previously thought due to shallow tropical hypoxia.