Sub-tidal, reef-lagoon surficial sediment samples from Discovery Bay, north Jamaica were analysed in order to quantify the impacts of anthropogenic bauxite inputs on trace metal (Fe, Zn, Mn) levels and sediment characteristics. Contaminant levels exhibit marked spatial variations, but are highest across central and southern parts of the bay and primarily reflect wind blown inputs, modified by subsequent suspended sediment transport. Highest contaminant levels (Fe—13,701 ppm, Mn—237 ppm, Zn—74 ppm) occur immediately adjacent to, and just north-east of, a bauxite loading terminal in the south-west of the bay. Sites of high sediment contamination are negatively correlated with per cent CaCO3 content, indicating the diluting effect of bauxite on the carbonate substrate. At high contamination sites CaCO3 levels are reduced to 63.7% and are in the range of 75–80% across much of the central and southern area of the bay. Magnetic susceptibility level measurements are positively correlated with iron and negatively correlated with CaCO3 content, and indicate the potential for using magnetic susceptibility measurements in metal contaminant tracing studies in carbonate environments. Whilst metal contamination levels are low compared with many clastic-dominated systems, and are currently at levels unlikely to impact the reef biota, the data indicate both the progressive contamination of this previously carbonate-dominated lagoon environment, and the potential for such terrestrial inputs to impact upon sediment characteristics in such restricted settings.