Determining how thermal variability will affect the structure, stability, and function of ecological communities is becoming increasingly important as global warming is predicted to affect not only average temperatures but also increase the frequency of long runs of high temperatures. Latitudinal differences in the responses of ecological communities to changes in their thermal regimes have also been predicted based on adaptations over evolutionary time to different thermal environments. We conducted an experiment to determine whether variability in temperature leads to consistent changes in community structure, temporal dynamics, and ecosystem functioning in laboratory analogues of natural freshwater supralittoral rock pool communities inhabited by meiofauna and zooplankton collected from sub-Arctic, temperate, and tropical regions. Thermal variability of +4 °C around mean temperature led to increased extinction frequency, decreases in consumer abundance, increases in temporal variability of consumer abundance, and shifts from predominately negative interactions observed under constant temperature to positive interactions in the temperate and tropical communities but not in the sub-Arctic communities. That sub-Arctic zooplankton communities may be more robust to thermal variability than temperate or tropical communities’ supports recent studies on macrophysiological adaptations of species along latitudinal gradients and suggests that increasing thermal variability may have the greatest effects on community structure and function in tropical and temperate regions.