The Oak Ridges Moraine aquifer feeds the headwaters of major rivers in the Greater Toronto Area and is an important source of domestic water supply. Recognizing the rapid rate of urban growth in the region, there is a concern that changing land use along the moraine must be strictly controlled if groundwater is to be adequately protected. To date, efforts to incorporate groundwater protection into the land use planning process have been hampered by an inadequate quantitative hydrogeological understanding of the aquifer system. Focusing on the Duffins Creek watershed, comprehensive hydrogeological studies including a numerical flow model now provide a quantitative insight into the hydrogeologic function of the moraine. These studies demonstrate that 60% of the entire basin groundwater discharge to streams occurs along the south flank of the moraine, and 60% of this headwater discharge occurs below the 275 m above sea level contour, one of the commonly accepted planning boundaries of the moraine. The remaining discharge is contributed by aquifers within and underlying deposits that extend to the south of the moraine. While 75–80% of the watershed discharge to streams is received from the uppermost aquifer, 20–25% is contributed by deeper aquifers underlying the extensive Northern–Newmarket till aquitard. This work shows that the moraine sediments represent just one component of a regional flow system that extends beyond the morphological boundary of the moraine. This has important implications for groundwater protection, as it demonstrates the need for management strategies that incorporate the regional groundwater flow system and not the moraine in isolation.