Disease represents an emerging threat to coral reef ecosystems worldwide, highlighting the need to understand how stressful environmental conditions interact with coral immune function and the structure of associated microbial communities to affect holobiont health. Reported increases in coral disease levels at sites adjacent to permanently moored platforms on Australia’s Great Barrier Reef (GBR) provide a unique opportunity to investigate environment-host-microbe interactions in situ. Here, we evaluate water quality (i.e. dissolved organic and inorganic nutrients), coral immune function (i.e. phenoloxidase activity) and coral-associated bacterial community structure (i.e. 16S rRNA gene amplicon sequencing) before, during and after a disease event that affected corals adjacent to reef platforms in the central (Whitsunday) sector of the GBR. Over the course of the 8-month study, 31% of tagged colonies of Acropora millepora adjacent to reef platforms developed signs of white syndrome (WS), while all conspecific, control colonies on a nearby reef remained visually healthy. Among the corals remaining visually healthy throughout the study, significant reductions in coral immune function and coral-associated bacterial diversity were recorded for those adjacent to reef platforms compared to those at the platform-free control site. Interestingly, two months prior to the first observation of macroscopic disease signs, bacterial diversity on corals that would develop WS was reduced, while heterogeneity in coral-associated bacterial communities among the group was significantly elevated relative to corals remaining healthy at the same location. These results indicate that proximity to reef platforms impacts coral immunocompetence and coral-associated bacterial community structure and diversity, which could profoundly affect the susceptibility of corals to disease.