A great deal of research has been conducted in temperate coastal ecosystems in order to understand the effect of anthropogenic inputs on the structure and function of the system; however, despite the fact that many tropical ecosystems are subject to increasing anthropogenic pressure, including increased nutrient and contaminant inputs, less attention has been paid to tropical regions. We present the results from a series of experiments aimed at examining the effects of Zn on microbial carbon fluxes in a tropical coastal ecosystem. We show that Zn additions at concentrations lower than the clean water limits set by environmental protection agencies for tropical waters can result in considerable changes in microbial carbon cycling in both the structure and function of the auto- and heterotrophic compartments. We observed a reduction in the relative proportion of diatoms and a concomitant increase in the relative proportions of other phytoplankton, notably dinoflagellates. Zn contamination resulted in a 2-fold increase in the amount of total primary production incorporated into bacterial biomass. This was concomitant with a reduction in the P:R ratio in the presence of Zn and ultimately resulted in a bacterially dominated, heterotrophic system. This shift in balance between production and respiration further pushes the system towards being a carbon source to the atmosphere rather than a sink. These results show that even low concentrations of Zn can have a negative effect on the lower levels of the food web and on carbon transfer in sensitive coastal environments.