Bioaccumulation is defined as the increase of contaminant concentrations in aquatic organisms following uptake from the ambient environmental medium. Different sources of exposure contribute to contaminant bioaccumulation. Toxicokinetic parameters are critical in the bioaccumulation processes, including the dissolved uptake rate constant, dietary assimilation efficiency, and efflux. Much study has been conducted on the quantification of these biokinetic parameters in diverse marine organisms. A well-developed biokinetic model then incorporates these biokinetic processes as well as contaminant geochemistry and animal physiology to predict bioaccumulation of contaminants in aquatic organisms. There are many applications of the biokinetic model in aquatic ecotoxicology, especially in understanding the change of contaminant concentration, which forms a fundamental basis in aquatic toxicology. Although biomonitoring programs have been established for decades, there are several caveats underlying the application of biomonitors given the multiple ecosystem stresses currently faced by coastal and estuarine ecosystems.