Hydrodynamic modelling of water movement in Hunts Bay, a protected part of Kingston Harbour, Jamaica, shows that depth averaged tidal flows are very low. In the northeast corner of Hunts Bay, water is essentially stagnant. Even under high flow conditions, much of the Bay bottom water is ‘bypassed' by buoyant, lower salinity surface flows. The muddy sediments of Hunts Bay reflect these sluggish to stagnant conditions; sediment cores from the northeast corner of the Bay contain progressively higher amounts of organic matter in their upper parts (last 15–20 years sedimentation). Combined C/N ratios and stable carbon isotope compositions of this organic matter imply a sewage origin. Both lead and chromium metal concentrations and enrichment factors relative to average crustal shales show geographically related patterns that reflect hydrodynamic circulation predicted by modelling. In particular, metal concentrations and enrichment factors are highest at the northern end of the bay, especially in the northeast corner. Modelling confirms that stagnant conditions would occur in the northeast part of the bay even without the presence of a major causeway. The causeway may contribute to low flow conditions, but is not the principal cause of organic contamination, which is simply an excessive input of sewage.