Marine heatwaves (MHWs) are intensifying globally, yet their risk to continental shelf seabed ecosystems remains poorly resolved. This research presents a spatial risk index (SRI) for MHWs and marine cold spells (MCSs) for seabed ecosystems between 30–500m on the East Australian coast. Using satellite SST data and a 26-year high resolution ocean hindcast model, MHW and MCS metrics across both the surface and the seafloor were aggregated with frequency, duration and intensity incorporated into the creation of the SRI. Furthermore, the SRI includes secondary modulators of seasonality and long-term warming, to heighten risk in regions with strong seasonal and interannual cycles. The SRIs reveal consistent divergence between surface and seafloor patterns, indicating a possible opportunity to use our understanding of ocean dynamics of the region to develop mechanistic explanations and predictive models of MHW and MCS occurrence. Regional contrasts demonstrate that no single spatial pattern characterises risk with differences across the EAC jet and the separation zone, where surface-based risk fails to represent subsurface dynamics. This challenges our current use of SST metrics for ecosystem management and highlights the importance of depth-resolved extreme event understanding, with direct implications for marine zoning, monitoring frameworks, and adaptive management under climate change.