Water quality deterioration caused by an enrichment in inorganic and organic matter due to anthropogenic inputs is one of the major local threats to coral reefs in Indonesia. But so far research emphasis of those unfavorable changes has often been put on processes along larger scales, e.g. across whole estuaries or entire shelfs. The present study investigated, for the first time in the Spermonde Archipelago, differences in water quality and bacterial community composition in several coral reef habitats, including the water column, particles and back-reef sediments, between a densely populated and an uninhabited island. The main aim was to elucidate if a) inorganic nutrients, chlorophyll a, dissolved organic carbon (DOC) and transparent exopolymer particles (TEP) differ between an uninhabited and a densely populated island of the archipelago and b) if there are differences in bacterial community composition in back-reef sediments and in the water column, which can be attributed to differences in water quality. Several key water quality parameters, including, PO4, chlorophyll a, DOC and TEP were significantly higher at the inhabited than at the uninhabited island. Flavobacteriaceae and various groups within the Gammaproteobacteria, bacterial taxa that are well adapted to organic matter rich environments, were significantly more abundant at the inhabited island. Within each of the sampled reef habitats variations in bacterial community composition between the islands could be attributed to differences in water quality. Copiotrophic bacterial taxa were enriched at the inhabited island with higher chlorophyll a, DOC and TEP concentrations. This study shows that the local island populations of the Archipelago can shape bacterial communities of the reef flats by altering the water quality of the surrounding waters. From a management perspective those quickly responding bacterial communities should become priority bioindicators for the implementation of sewage treatment facilities.