Quandamooka Sea Country (Moreton Bay) supports many long standing, high-latitude coral reef communities proximal to urban development. However, recent flooding events have caused prolonged changes to water quality in the bay, due to its limited tidal flushing. The spatial and seasonal dynamics in coral reef community response to flooding within this unique system are not yet fully understood. Here, we compare the status of sub-tidal benthic communities across three seasons surrounding the 2022 severe flooding event and investigate relationships with water quality parameters. Benthic community data from assemblages within four sites across the bay were captured using photogrammetry, reconstructed using 3D modelling and analysed using quadrat point annotation. Community diversity and total Scleractinian cover decreased significantly across the bay after the floods. This response was more pronounced in sites experiencing larger decreases in salinity and increases in turbidity, which were also proximal to the Logan River mouth. Acropora species experienced the largest reductions in cover following the floods, with live Acropora colonies almost completely removed from Peel and Goat Island reefs after the floods. These results suggest that further benthic community change in Quandamooka can be expected as severe rainfall and flooding events become more frequent due to climate change.