Within coral reefs, different thermal environments can be found at locations separated by less than 100 s of meters and can generate fine-scale patterns of thermal stress and subsequent bleaching. In this study, we use an 11-month record of in situ temperature measurements, coupled with oceanographic and atmospheric data to examine the role of surface and advective heat fluxes in driving spatial patterns of temperature variability across several reef zones (i.e., fore-reef, reef flat, channel and lagoon) within an individual coral reef atoll. We show that advection of heat (driven by a combination of wave and tidal flows) was dominant across all sites and surface heating was more important across shallow areas or areas of low net exchange (i.e., reef flat and lagoon zones). Tidal flows were important in driving short term variability in the transport of heat across the atoll, but their contribution to the net transport of heat (cooling vs heating) was less significant over the longer timescales (days to weeks) that are typically used to assess thermal stress experienced by coral reef communities (e.g., Degree Heating Weeks). Conversely, although the wave-driven advection of heat contributed minimally to reef temperature changes over short timescales, the net transport of heat over daily to weekly timescales had a significant influence on persistent temperature anomalies. By parameterising the mechanisms driving temperature variability across the reef flat and lagoon zones, we demonstrate how satellite measurements of sea surface temperatures can be corrected to provide robust temperature estimates at the reef scale.