Coral reef calcification rate is an ecological metric that integrates the effects of multiple stressors on coral population health. Here, we predicted and compared the spatial patterns of coral reef calcification rate, mediated by light availability and carbon chemistry, across the Great Barrier Reef (GBR) for March 2011 (a month after Cyclone Yasi), March 2012 (near the end of a La Niña event), and March 2015 (start of an El Niño event). These predictions were obtained by combining the CSIRO Environmental Modelling Suite with a new mechanistic biological model of acidification- and light-mediated coral reef calcification, calibrated to laboratory data, that can produce probabilistic forecasts. Across the GBR, this targeted combination of models predicted reductions in calcification rate following wetter conditions, surprisingly even in offshore areas. Using model scenarios that separated out the localised impacts of acidification and water turbidity, we found that both impacts substantially modified the predicted calcification rates, although the present-day effects of water turbidity were stronger than acidification, and localised cumulative effects were stronger inshore than offshore. Our results highlight the large spatial footprint of severe weather events on coral reef calcification processes in the GBR, arising from reduced water quality driven by riverine discharges.