The ephemeral rivers in northern Australia break up into a series of waterholes during the long dry summer season. These in-stream waterholes provide vital habitat for the survival of aquatic biota during this period. We describe how high-time-resolution (20 min) waterhole temperature measurements made in the Flinders and Gilbert Rivers in tropical northern Australia were used to derive thermal frequency curves that show how often waterhole temperature exceeded any given temperature threshold. During the summer period, temperatures near the surfaces of waterholes were often above that suitable for the optimum growth of some tropical fish (31°C). At the bottom of waterholes this exceedance occurred less often, and in turbid waterholes that were stratified, temperatures rarely exceeded this threshold. Temperatures that could be lethal to some fish (34°C) also were exceeded at the surface of waterholes, but rarely, if ever, at the bottom of the waterholes. An energy-balance model was used to estimate daily mean waterhole temperature with good accuracy (±1 K) at all but the sites where wind speed may have been >2 m/s (assumed in the model). The model also was used to predict the effects of climate change on waterhole temperature and the change in exeedance of thermal thresholds. A 2°K climate warming raised waterhole temperature by ~1°K. However small this increase might seem, it led to a doubling of the length of time water temperatures were in excess of thresholds around 31°C.