Coral reefs are suffering a long-term global decline, yet the causes remain contentious. The role of poor water quality in this decline is particularly unclear, with most previous studies providing only weak correlations between elevated nutrient levels and coral mortality. Here we experimentally show that routinely measured components of water quality (nitrate, phosphate, ammonia) do not cause substantial coral mortality. In contrast, dissolved organic carbon (DOC), which is rarely measured on reefs, does. Elevated DOC levels also accelerate the growth rate of microbes living in the corals’ surface mucopolysaccharide layer by an order of magnitude, suggesting that mortality occurs due to a disruption of the balance between the coral and its associated microbiota. We propose a model by which elevated DOC levels cause Caribbean reefs to shift further from coral to macroalgal dominance. Increasing DOC levels on coral reefs should be recognized as a threat and routinely monitored.