<span style="font-weight: 400;">Marine heatwaves (MHWs) disrupt ecosystems across multiple trophic levels by altering oxygen and biological productivity through the water column. Yet, most studies focus on the surface, overlooking subsurface processes that shape ecosystem responses, particularly under compound events involving multiple co-occurring extreme environmental conditions. To address this gap, we analysed 16 years of routine and event-based glider observations on the continental shelf around Australia to present the first comprehensive assessment of the subsurface biogeochemical response during surface MHWs across four contrasting coastal regions. Summer surface MHWs were characterised by a shallower mixed layer depth than normal conditions and enhanced stratification, confining warming to the upper ocean, while other seasons allow deeper penetration under weakly stratified conditions. Stratification favoured deeper and intensified deep chlorophyll maxima, aligned with the depth of stratification maxima, and emerged as a useful proxy for the vertical extent of MHWs. Across all regions and seasons, for non-MHW conditions, dissolved oxygen had a bimodal distribution above and below the mixed layer. However, this distribution changed with event severity and included greater concentrations of low dissolved oxygen and reduced concentrations of high dissolved oxygen during strong events. Below the mixed layer, the bimodal distribution was less apparent and oxygen concentrations during strong events were more concentrated towards middle values. During moderate and strong MHWs, chlorophyll concentrations declined in the mixed layer, albeit this trend was not apparent below it. Regional responses were related to the environmental setting, including the continental shelf structure and boundary current influences, underscoring the importance of region-specific monitoring to understand how MHWs influence biogeochemistry, and furthermore, their ecological consequences on coastal waters. The interaction between physical processes, such as seasonal circulation and stratification, and biological feedback, including the presence of deep chlorophyll maxima and potential oxygen production, highlights the complex biogeochemical responses to MHWs. </span>