The balance between development and resource conservation is a major challenge facing many Canadian communities. The hydrologic cycle of most watersheds in the Toronto region has undergone a fundamental change in the past 50 years due to increased urban cover. Reduced infiltration and increased stormwater runoff carrying sediment and urban contaminants to semi-closed coastal lagoons and wetlands along Lake Ontario threaten these fragile ecosystems. Paucity of existing information and poorly understood interactions between groundwater and surface water flow make it difficult to identify problems and manage urban water systems. A conceptual model of the Pleistocene geology combined with three-dimensional modeling of groundwater flow (FEFLOW) is used to quantify the regional groundwater flow system and delineate recharge and discharge zones in the Frenchman's Bay watershed east of Toronto. This study demonstrates the necessity of combining detailed hydrostratigraphic analysis with groundwater modeling to better understand regional groundwater flow systems and their appropriate incorporation into the land use planning stage of urban development.