Sea surface temperature observations have shown that western boundary currents, such as the East Australian Current (EAC), are warming faster than the global average. However, we know little about coastal temperature trends inshore of these rapidly warming regions, particularly below the surface impacting biologic habitats. Here we use long-term in situ temperature observations through the water column at five southeast Australia coastal sites, including the long-term Port Hacking and Maria Island national reference stations, to estimate warming trends between the ocean surface and the bottom. Using an advanced trend detection method, we find accelerating warming trends at multiple depths in the EAC extension region at 34.1 and 42.6° S. We see these accelerating trends at the surface and bottom at 34.1° S, and at 2 depths in the top 50 m at 42.6° S. The spatial and temporal variability in the long-term temperature trends highlight the important role of regional dynamics against a background of broad-scale ocean warming. Moreover, considering that recent studies of ocean warming typically focus on surface data only, our results show the necessity of subsurface data for improved understanding of regional climate change and potential impacts on biological processes.