Temperature perturbations from climate change affect ecosystems through short-term pulse events, such as heatwaves, and chronic long-term shifts. Temperate rocky reef ecosystems have been observed to show substantial ecological change as a result of short-term temperature fluctuations, but the longer-term impacts of temperature change remain poorly understood. Here, we investigate temperate reef fishes and mobile invertebrates along Tasmania's east coast, contrasting trends in species richness, abundance, and community structure across seasons within a year to those observed over three decades of warming. Fishes exhibited dynamic seasonal shifts, but interannual changes in richness and abundance balanced out over decades with limited overall net change. In contrast, invertebrate communities changed little seasonally but suffered significant long-term losses. Our study revealed short-term ecological changes driven by temperature to be incongruent with long-term shifts. Species responded in varying ways, depending on life history and ecology. Fishes apparently tracked short temperature pulses, while less mobile invertebrates, such as echinoderms and molluscs, tolerated short-term fluctuations but exhibited long-term decline. Multi-scale studies across a broad range of taxa are needed to clarify thermal responses. The most vulnerable taxa—those facing long-term thermal stress—may be overlooked through decisions based on short-term studies, risking major biodiversity loss.