We present results of the thermodynamics and hydrodynamics of an atoll system and their effect on coral cover based on field measurements from 2012 to 2014 on Palmyra Atoll in the central Pacific. We found that spatial variations in coral cover were correlated with temperature variations on time scales of days to weeks. Shallow terrace and backreef sites with high coral cover (> 50%) had a highly variable temperature distributions, but their average weekly temperature distributions were lower and similar to offshore waters. The mechanism for maintaining this low weekly temperature was mean advection, which varied on a weekly timescale in response to wave forcing. Tides were also important in driving flow on the atoll, but their contribution to the net transport of heat was not significant. Wind and regional forcing were generally not important in driving flow inside the atoll. Buoyancy‐driven flows were important within the lagoons, and in driving cross‐shore exchange on forereef environments. The physical factors favoring high coral cover percentage varied according to the different prevailing hydrodynamic regimes: low temperatures in backreef habitats, short travel times in lagoon habitats (days since entering the reef system), and lower wave stress on forereef habitats. In light of future warming from climate change, local areas of reefs which maintain lower temperatures through wave‐driven mean flows will have the best likelihood of promoting coral survival.

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