Mass coral bleaching has emerged in the 21st century as the greatest threat to the health of the world's reefs. Dinoflagellates of the family Symbiodiniaceae form mutualistic symbioses with reef-building corals, but also inhabit reef environments as free-living cells. The fate of the expelled zooxanthallae is critical in understanding recovery in coral reef ecosystem. Here we use a model of zooxanthellae that explicitly represents the processes of inorganic nutrient acquisition, photoadaptation, xanthophyll cycle dynamics, and reaction centre state transitions. The model is embedded in a hydrodynamic-sediment-biogeochemical model of the Great Barrier Reef ecosystem (eReefs), allowing representation of (1) expulsion of cells into the water column; (2) passive transport of the expelled cells due to ocean circulation; (3) porewater exchange between the water column and sediment; (4) active migration to the coral surface and uptake by the coral animal; and (5) growth and grazing mortality while in the free-living phase. We simulated the GBR bleaching event of 2017 with a 1 km configuration. Simulations show that expelled zooxanthallae are advected from the site of expulsion and become embedded in the sediments. The ability for expelled zooxanthellae and their progeny to inoculate new hosts is strongly influenced by local oceanography.