Cycling of glucose at the sediment–water interface was determined through coupling measurement of natural substrate concentrations with heterotrophic uptake by the natural microbial communities in the sediment and in the water column. The same general pattern was found for both polluted and less polluted parts of Toronto Harbour, so that other labile organic species possibly have similar cycles. Velocity of uptake of glucose (flux) and turnover time showed no relationship to either substrate concentration or total organic matter of the sediments. Activity in the water column could be supported to a major extent by sediment export of substrate by turbulent diffusion. Sediment activity must be supported by particulate sedimentation and hydrolysis of large organic molecules, which may be aided by the macrobenthic community. Pollution stress apparently alters the catabolism of the substrate. The observed substrate concentrations may reflect a minimum of residual concentration, below which the microbial community has difficulty in taking up the substrate.