<p>Marine heatwaves (MHWs) and marine cold-spells (MCSs) can negatively impact biodiversity as species distributions are largely governed by temperature linked to physiological tolerances. These extremes have not been considered in South Africa’s Marine Protected Area (MPA) network design, so understanding frequency and severity of extreme thermal events will be important for assessing their impact. This study characterises MHWs and MCSs in MPAs across the six South African marine ecoregions, using a novel index to compare thermal event severity. Thermal events declined in duration and intensity from west to east, with the least severe events recorded in the Delagoa ecoregion. Walker Bay MPA was identified as most at risk due to the combined impact of MHWs and MCSs. These thermal events may threaten the ability of the MPA to meet its conservation objective as a cetacean sanctuary. If past trends in MHW frequency and cumulative intensity persist, the majority of South African MPAs could experience more severe heatwaves in the future. Our approach will help prioritise sites for in situ monitoring of water temperature and studies of the impact of extreme thermal events, as well as identifying areas for expanding refugia and conservation corridors, supporting adaptive management into the future.</p>