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Abstract An understanding of the combined effects of climate change (CC) and other anthropogenic stressors, such as chemical exposures, is essential for improving ecological risk assessments of vulnerable ecosystems. In the Great Barrier Reef, coral reefs are under increasingly severe duress from increasing ocean temperatures, acidification, and cyclone intensities associated with CC. In addition to these stressors, inshore reef systems, such as the Mackay–Whitsunday coastal zone, are being impacted by other anthropogenic stressors, including chemical, nutrient, and sediment exposures related to more intense rainfall events that increase the catchment runoff of contaminated waters. To illustrate an approach for incorporating CC into ecological risk assessment frameworks, we developed an adverse outcome pathway network to conceptually delineate the effects of climate variables and photosystem II herbicide (diuron) exposures on scleractinian corals. This informed the development of a Bayesian network (BN) to quantitatively compare the effects of historical (1975–2005) and future projected climate on inshore hard coral bleaching, mortality, and cover. This BN demonstrated how risk may be predicted for multiple physical and biological stressors, including temperature, ocean acidification, cyclones, sediments, macroalgae competition, and crown of thorns starfish predation, as well as chemical stressors such as nitrogen and herbicides. Climate scenarios included an ensemble of 16 downscaled models encompassing current and future conditions based on multiple emission scenarios for two 30‐year periods. It was found that both climate‐related and catchment‐related stressors pose a risk to these inshore reef systems, with projected increases in coral bleaching and coral mortality under all future climate scenarios. This modeling exercise can support the identification of risk drivers for the prioritization of management interventions to build future resilient reefs.Integr Environ Assess Manag2024;20:401–418. © 2023 Norwegian Institute for Water Research and The Authors.Integrated Environmental Assessment and Managementpublished by Wiley Periodicals LLC on behalf of Society of Environmental Toxicology & Chemistry (SETAC). This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.