Thermally driven bleaching events are a growing concern for reef ecosystems across the tropics. To assess and predict thermal stress impacts on reefs, remotely observed sea surface temperature (SST) commonly is used; however, reef communities typically extend to depths where SST alone may not be an accurate measure of in situ variability. Here nearly two decades of temperature observations (2‐ to 90‐m depth) at three stations around Palau are used to develop an empirical model of temperature variability versus depth based on SST and sea level anomaly (SLA). The technique yields depth‐averaged R2 values >0.88, with SLA predicting fore reef temperatures near the thermocline and SST capturing upper mixed layer temperatures. SLA complements SST by providing a proxy for vertical isotherm displacements driven by local and remote winds on intraseasonal to interannual time scales. Utilizing this concept, thermal stress on corals can be predicted from the surface through the mesophotic zone.