In northern Australia in-channel waterholes in ephemeral rivers provide vital habitat for the survival of fish during the dry season. Many aspects of the water quality of these waterholes can affect habitat suitability, but water temperature is arguably the single most important parameter, since it directly affects the rates of many important physical, chemical and biological processes. In-channel waterhole temperature was monitored at a number of locations in the Flinders and Gilbert catchments as the dry season evolved in 2012/13. These data were used to derive frequency curves that show how often water temperature exceeded any given temperature threshold. To explore how often waterhole temperature may become detrimental to fish, the exceedance times for preliminary thresholds for optimum growth and lethal effects are presented. How these exceedance times increase under a future warmer climate is also illustrated using an energy balance model that can estimate water temperature from daily weather data.