Coral reefs are being impacted by both local and global human-induced stressors. To understand and quantify how environmental impacts correlate to changes in reef communities, long-term monitoring is a necessity. Most reef monitoring programs implement visual surveys (i.e. coral cover, bleaching or disease assessments), yet visual cues become evident at a point when ecosystem change may be irreversible and management interventions are compromised. Marine microbial communities respond rapidly to environmental shifts and represent a potential early warning indicator of ecosystem stress. Here we detail how free-living microbes can be used in reef monitoring, through collection of seawater and sediments at 50 sites across the GBR for metagenomic and metatranscriptomic sequencing which is paired with AIMS-LTMP in situ reef health surveys. Direct correlation of the microbial taxonomic and functional signatures with environmental data on benthic cover and water quality was undertaken. Our results indicate that Synechococcus/Prochlorococcus relative abundance ratios may be utilised as an index of eutrophication, and that Flavobacteriaceae (phylum: Bacteroidetes) correlate to the reefs with increased temperature and nutrient loads. Microbial observation may be crucial for future development of diagnostic microbiome-based tools in reef conservation, restoration and management efforts.