The estimation of base flow contributions to streamflow, and in particular the partitioning of base flow into shallow and deep aquifer components, is a challenging problem in water resources management. In this study, the newly developed hillslope-storage Boussinesq analytic-element (hsB/AE) model is applied to the Allen River headwater catchment in southern Quebec, Canada, which is a major recharge area for the transboundary Chateauguay River watershed. This first application to a real catchment serves as an illustration of the basic principles behind the coupled model and an investigation into interaquifer interactions and the origins of base flow contributions to streamflow. The hsB component of the model represents local groundwater flow in sloping, shallow Quaternary sediments, whereas the AE component represents the underlying regional bedrock aquifer. The catchment is partitioned into hillslopes of regular convergent, divergent, or combined planform shapes. Simulations are run for the summer periods of 2008 and 2009, and the resulting base flows show good correspondence with estimates on the basis of standard hydrograph separation techniques, in particular, those for low-flow periods from July to September. Overall, satisfactory matches are obtained for the bedrock aquifer heads, but with some underestimation of heads further away from the river. In terms of exchanges between the aquifers, 95% of total leakage is directed toward the bedrock aquifer, whereas only 5% flows in the reverse direction and feeds the hilllsope aquifer, especially in the steeper portion of the catchment. The simulated base flow is partitioned into roughly 65% originating from the shallow hillslope aquifer and 35% from the deep bedrock aquifer, with small interannual variations on the order of 3-5%. This ratio is relatively insensitive to changes in parameter values. For example, a 50% decrease in aquitard thickness reduces the deep bedrock aquifer contribution by only 12%.