Microbes play a critical role in nutrient-deplete habitats such as coral reefs, where they mediate efficient nutrient recycling. With reefs under increasing pressure from environmental changes, a greater understanding of microbial contributions to reef health is urgently needed. The Integrated Marine Observing System (IMOS) Great Barrier Reef Microbial Genomics Database (GBR MGD) was established to provide high-quality genomic references to increase our understanding of the role of microbes in reef environments. Sample collections from 48 sites on the GBR and a hybrid assembly process was used to combine Illumina and Nanopore sequencing data to generate ~5000 microbial genomes, complemented with comprehensive water chemistry and benthic reef survey data. Microbes and their functions were correlated to changes in temperature, water chemistry, benthic survey coverage, and reef zoning status. The GBR MGD is now being used to profile changes in microbial community and function during the 2024 GBR mass bleaching event, to identify microbial prognosticators of reef recovery. The GBR MGD provides the much-needed framework for development of novel informative monitoring metrics for future reef management efforts focussed on environmental change and intervention activities.