An important, yet poorly understood, influence on the hydrologic behaviour of mountain headwater streams is deep groundwater (DG) flow, which circulates at depth through the bedrock system and discharges to surface water or shallow groundwater at stream valleys. In this study, two- and three-dimensional hydrogeological models were generated for both generic and real topography. DG contribution areas were delineated using groundwater pathline analysis, and the sensitivity of DG discharge at headwater stream valleys due to changes in applied recharge was investigated. For some streams, the 3-D nested nature of topographically-driven DG flow results in groundwater that is recharged within one headwater stream catchment bypassing the associated stream valley and emerging as DG discharge in a different, relatively deeper stream valley. Contributing areas of DG to headwater streams are thus more complex than would be predicted based on catchment boundaries alone. Differences in DG discharge and DG contributing areas in response to changes in applied recharge are a reflection of differences in topography and suggest that headwater streams within the same watershed differ in their sensitivity to changes in recharge. A small, but significant, temporal response of DG discharge to a change in recharge is found to occur within a 1 to 3 year timeframe, highlighting the importance of variations in DG discharge for stream hydrology. The modelling approach used in this study requires only digital elevation model data, and thus can be used in regions of limited data and in ungauged basins to provide a preliminary indication of relative stream sensitivity to long-term changes in recharge as a result of climate change, forest management practices, or groundwater extraction. © 2012 Canadian Water Resources Association.