A mass balance model of contaminant fate and transport was developed for, and applied to the Bay of Quinte and its food web. The loadings, fate and persistence of 4 metals and 20 HOCs were quantified, analyzed and compared with previous models of the system (Diamond et al. 1994, Diamond et al. 1996, Morrison 1998). The effect of phosphorous concentrations on the fate and transport of sumPCB in the Upper Bay was investigated. Chemicals originated from tributaries (metals, PCBs), atmosphere (dioxin, furan, DDT), Lake Ontario (dieldrin, atrazine) and point and non-point sources (17beta-estradiol, BDE-47, HCB, benzo[a]pyrene). Loadings of most chemicals decreased from 1990 to 2000. In response, metal water but not sediment concentrations decreased. Chemicals are mainly lost from the system by export. Increases of phosphorus will increase chemical sedimentation and hence sediment but not water concentrations.