While, in lower latitudes, population-level differences in heat tolerance are linked to temperature variability, in the Southern Ocean remarkably stable year-round temperatures prevail. Temporal variation in the physiology of Antarctic ectotherms is therefore thought to be driven by the intense seasonality in primary productivity. Here we tested for differences in the acute upper temperature limits (lethal and activity) of 2 Antarctic marine invertebrates (the omnivorous starfish Odontaster validus and the filter-feeding clam Laternula elliptica) across latitude, seasons and years. Acute thermal responses in the starfish (righting and feeding) and clam (burrowing) differed between populations collected at 77° S (McMurdo Sound) and 67° S (Marguerite Bay). Both species displayed significantly higher temperature performance at 67° S, where seawater can reach a maximum of +1.8°C in summer versus −0.5°C at 77° S, showing that even the narrow spatial and temporal variation in environmental temperature in Antarctica is biologically meaningful to these stenothermal invertebrates. Temporal comparisons of heat tolerance also demonstrated seasonal differences in acute upper limits for survival that were consistent with physiological acclimatisation: lethal limits were lower in winter than summer and higher in warm years than cool years. However, clams had greater inter-annual variation of temperature limits than was observed for starfish, suggesting that variation in food availability is also an important factor, particularly for primary consumers. Teasing out the interaction of multiple factors on thermal tolerance will be important for refining species-specific predictions of climate change impacts.