<p>Coral bleaching represents a primary threat to coral reefs worldwide. Patch reefs in lagoon systems are highly susceptible to bleaching due to shallow, high residence water, high light intensity and reef edge effects. Geomorphic, spatial and hydrodynamic factors are important in modifying environmental stressors, yet their interacting roles in influencing bleaching responses are not well understood. In this study, we investigated the importance of patch reef shape, edge complexity, position, relief, aspect, current flow and legacy (previously dead coral) factors as predictors of thermal stress-induced bleaching and mortality at One Tree Island in the southern Great Barrier Reef. We observed extensive coral bleaching across all 26 surveyed patch reefs, all genera and all growth forms, with a high proportion (88%) of coral cover being either bleached or recently dead. Bleaching mortality index (BMI) varied strongly with growth form and was moderated by the complexity of patch reef aerial-view 2-dimensional shape, distance from the platform reef crest and current flow speed. Low-complexity, low-flow patch reefs located in the middle of the lagoon system were the most impacted, whilst patch reefs with high flow near the reef crest were the least impacted by bleaching. Our study demonstrates that local hydrodynamic and geomorphological conditions can strongly influence bleaching outcomes, even within a single platform reef system, and highlights the importance of incorporating interacting effects of patch reef shape, position and water flow when predicting and managing the impacts of future marine heatwaves.</p>