At a time of rapid global change, a socio-ecological system (SES) approach can provide a framework through which to quantify and communicate the risks and uncertainties of coupled human-natural systems. Islands, and tropical coral reef islands in particular, can be excellent models for SES research since they may be considered as both closed and open systems, where agents-- both human and nonhuman--and their interactions, may be considered at a variety of spatial and temporal scales and with diverse levels of complexity. Bacteria and Archaea communities are the executants of biochemical cycling in systems, and alterations in the structure of microbial communities can provide indications of system-wide metabolic shifts driven by natural and human forces. In this thesis, I first present patterns of spatial and temporal variability in microbial communities across a tropical coral island reefscape, where I hypothesized: Microbiome host, habitat and sampling location will house distinct microbiomes (beta diversity) that differ between seasons. Microbiomes were primarily host specific, and host specificity varied with structural scale: microbiomes of reef sediment, seawater and corals were different from each other. Zooming in, the three species of corals examined also had distinct microbial communities associated with them. These host specific microbiomes varied differentially across spatial scale, such as island side, reef habitat (fore, back and fringing reefs) and sampling locations. The structure of coral microbiomes supported evidence of a core microbiome with low species richness and a less-abundant but greatly richer resident microbiome or environmentally responsive community. Of 476 taxonomic families identified in our samples, sequences of the Family Endozoicamonaceae dominated all coral microbiomes, representing between 68-80% of the relative abundance of bacteria and archaea depending on species and varying less than 1% across reef habitats. Considering all coral species together, this meant that the bulk of coral microbiome richness made up less than 13% of the total microbiome. The top ten most relatively abundant families in each coral species across habitats and seasons showed that each host- and spatially distinct microbiome experienced seasonality differently. These shifts were contextualized within the scope of the Mo’orea Island Socio-Ecological system. Because coral microbiomes are sensitive to biophysical fluxes, coral microbiome diversity estimates (Chao1) were interpolated into an islandwide heatmap. By comparing and locating areas of anomalous microbiome diversity with locations of biophysical anomalies around the island, such as increased nitrogen concentrations, we found that locations of convergent anomalies were situated near to areas of increased human activity, although uncertainty exists as to at what extent and whether human activity is a directly causative effect. However, our maps do provide evidence for the integration of human and natural systems at local to microbial scales.