Microorganisms play a fundamental role in the functioning and stability of coral reefs and are often the first to respond to perturbations in the environment. With coral reefs becoming increasingly threatened by localised impacts (e.g declining water quality) and global pressures from climate change, shifts in the composition and function of microbial communities can provide crucial diagnostic information on the extent of these impacts. To explore the potential of seawater and sediment microbial communities to inform water chemistry measurements, the Integrated Marine Observing System (IMOS) Australian Microbiome Initiative has recently established the IMOS Microbial Observatory (IMOS-MO) stations at key inshore and offshore reef sites of the Great Barrier Reef. Within the IMOS-MO stations, extensive metagenomic and metatranscriptomic data were collected alongside water chemistry and benthic cover measurements to identify how microbial activity is changing with shifting environmental parameters across space and time. Using multi-omic integration approaches, we successfully identified molecular signatures of opportunistic microbial function and activity associated with nutrient enrichment in degraded inshore reefs. The IMOS-MO resource establishes reef-associated microbial observatories in the GBR, and data collected to date suggest that seawater/sediment microbial communities are associated with reef health, warranting detailed investigation into marine microbes and reef function.