We examined the seasonal and spatial variability in the temperatures of nearshore reef waters over 19 months across Coral Bay at Ningaloo Reef, Western Australia. Local deviations in the mean daily temperature of nearshore reef waters from offshore values (DT) were a linear function of the combined effect of net atmospheric heating (Q net ) and offshore wave height and period H s ffiffiffiffi ffi t p p . Whereas intra-annual variation in local heat exchange was driven mainly by seasonal changes in shortwave radiation, intra-annual variation in local cooling was driven mostly by changes in relative humidity (r 2 5 0.60) and wind speed (r 2 5 0.31) that exhibited no apparent seasonality. We demonstrate good agreement between nearshore reef temperatures modeled from offshore sea surface temperatures, offshore wave forcing, and local atmospheric heat fluxes with observed temperatures using a simple linear model (r 2 5 0.31-0.69, root-mean-square error 5 0.4-0.9uC). Using these modeled nearshore reef temperature records, we show that thermal stresses across the reef reached between 16uC weeks and 22uC weeks in the summer of 2011 when a mass coral bleaching event was reported, and between 12uC weeks and 13uC weeks in the following summer of 2012 when no mass bleaching was reported. After compensating for differences between observed and modeled thermal stresses, we found that maximum thermal stresses across the reef likely reached as high as 18-34uC weeks in the summer of 2011. The approach used here could thus improve our ability to predict spatial variation in thermal stress and bleaching across other wavedriven nearshore reef systems.