A multi-segment model of chemical fate and transport in the Bay of Quinte and a food chain model that simulate average annual conditions, are used to examine the behavior of arsenic (As), pentachlorophenol (PCP) and polychlorinated biphenyls (PCBs) in the Bay, an ''Area of Concern'' in the Great Lakes. The Bay model was used to predict the status of As and PCP from known loading data, but for PCBs with unknown loadings, the Bay and food chain models were used to ''back-calculate'' total loadings to the Bay. Chemical behavior depends on the characteristics of the Bay and physical-chemical properties of chemicals. Short water residence times of less than a week to several months result in chemicals being advected, unless subject to other, more rapid processes. In Upper Bay, rapid rates of sediment deposition and resuspension retard losses by advection of persistent chemicals such as PCBs and As, despite As being largely dissolved in the water column. Overall, behavior in Upper Bay is dominated by sediment-water exchange, and in Lower Bay by water exchange with Lake Ontario. Because of PCP's rapid transformation rate in the water column, most chemical is transformed before it reaches the sediments or downstream segments. It is recommended that elevated As inputs from the Moira River must be controlled to reduce in-Bay water and sediment concentrations, and for PCP, industrial discharges must be reduced. If reduced, concentrations in the Bay would respond within 3 months, I month and 3 years in the water, and about 6, 3 and 10 years in sediments for As, PCP and PCBs, respectively.