The Ontario Clean Water Act (2006) mandated that eight and two municipal drinking water intakes in the Cataraqui Region Conservation Authority (CRCA) and the Ganaraska River Source Protection Agency (GRSPA) jurisdictions respectively, be protected from contaminants released into the surrounding waters through the delineation of Intake Protection Zones (IPZs). Toward these objectives, the Estuary and Lake Computer Model (ELCOM) was applied to simulate the hydrodynamics and contaminant transport in the eastern Lake Ontario and upper St. Lawrence River. Model hydrodynamics were comprehensively validated against field data collected during April-October, 2006. The flow was found to be predominantly wind induced in the southwestern lacustrine portion of the domain and hydraulically driven in the northeastern riverine portion with storm events resulting in river flow reversals. The modeled surface currents were applied to delineate IPZs surrounding the drinking water intakes. Passive tracers were simulated as surrogates for combined sewer outflows, tributary flows, municipal/wastewater and industrial discharges identified by CRCA as threats to drinking water intakes. Wind was found to be the most dominant forcing to transport contaminants, both in the Kingston Basin and the St. Lawrence River, whereas the St. Lawrence River outflow was found to influence the transport of contaminants along the river. The hydrodynamics and contaminant transport in the near-shore region of Lake Ontario, from Port Hope to Cobourg was also simulated using ELCOM and the results were comprehensively validated against field data collected during April-September, 2010. Upwelling and downwelling events caused by south-westerly and north-easterly winds were found to be the predominant hydrodynamic process. These events generated barotropic geostrophic alongshore currents or ‘coastal jets’ of ~20 cm s-1. Discharges from river plumes and sewage treatment plants were simulated as tracer releases. The tracer concentrations were primarily influenced by the close proximity of the intakes to the effluent release points, the volume and direction of the discharge from the intakes and the physical processes driving the flow dynamics. / Thesis (Ph.D, Civil Engineering) -- Queen's University, 2013-07-17 11:41:54.68