This paper reviews current knowledge of biogeochemical cycles of pollutant organic chemicals in aquatic ecosystems with a focus on coastal ecosystems. There is a bias toward discussng chemkal and geochemical aspects ofbiogeochemical cycles and an emphasis on hydrophobic organic compounds such as polynuckar aromatic hydrocarbons, polychlorinated biphenyls, and chlorinated organic compounds used as pesticides. The complexity of mixtures of pollutant organic compounds, their various modes ofentering ecosystems, and their physical chemical forms are discussed. Important factors that influence bioavailability and disposition (e.g., organism-water partitioning, uptake via food, food meb transfer) are reviewed. These factors include solubilities ofchemicals; partitioning ofchemicals between solid surfaces, colloids, and soluble phases; variables rates of sorption, desorption; and physiological status of organism. It appears that more emphasis on considering food as a source of uptake and bioaccumulation is important in benthic and epibenthic ecosystems when sediment-associated pollutants are a nt source ofinput to an aquatic ecosystem. Progress with mathematical models for exposure and uptake of contaminant chemicals is discussed briefly.