The Great Barrier Reef (GBR) coral coverage is in rapid decline from severe and sustained pressures from lagoon water quality, crown-of-thorns starfish (COTS), coral bleaching, tropical cyclones, pollution and diseases. The two recent GBR coral bleaching events (2016–2017) lead to Great Barrier Reef Marine Park Authority (GBRMPA) shifting their focus from passive management to active intervention (Great Barrier Reef Blueprint for resilience by GBRMPA). These active interventions, potentially able to increase GBR resilience, as there are reefs that, due to their physical location relative to all other reefs, river and estuary entrances, ocean currents, have favourable coral growth conditions. To undertake such interventions, various information is required including tropical cyclone wave climates. This paper develops tropical cyclone wave climates for the entire GBR. These wave climates were developed by simulating several thousand synthetic cyclones derived from the “HadGEM” general circulation model with RCP8.5 climate change scenario. The synthetic cyclones adopted herein include the following climate changes assessed by comparing averages of key forcing parameters between 1950 to 1999 and 2050 to 2099. Their average arrival rate increases from 2.25 to 2.41 cyclones/year and their average maximum wind speed increases from 24 to 28 m/s. Their average radius to maximum winds remains constant at 51 km. Two key challenges were resolved, namely, long runtimes and large files (600 m grid increment covering 1800 km by 280 km). Runtimes were reduced by excluding cyclones where their wind speeds over the entire event never exceeded 10 m/s within GBR itself or within 100 km of the GBR over water. Maximum wave heights were compared with an extended fetch empirical expression, which was based on satellite data of tropical cyclones in open waters, when cyclones were outside the GBR lagoon. These comparisons indicate that predicted wave heights have a lower bias using default wave generation parameters when compared with the extended fetch empirical expression. Prediction uncertainty was estimated at no more than 10% from various cyclonic wind-field models. The existing GBR reefs reduce nearshore wave or runup height by between 1.5 and 2 times compared to the no reef case. The reduction in wave or runup height was found to be minimal for 1 m sea level rise. These two findings indicate that there is more flooding potential from coral removal than SLR within the GBR lagoon.