On-going geological disposal programs for spent nuclear fuel have generated strong demands for investigation and characterization of deep-lying groundwater systems. Because of the long time scales for which radiological safety needs to be demonstrated in safety assessment applications, an analysis of the hydrogeological performance of the geosphere system during glacial climate conditions is needed. Groundwater flow at depth in crystalline rock during the passage of an ice-sheet margin is discussed based on performed groundwater-flow modeling of two bedrock sites, Forsmark and Laxemar, in the Fennoscandian Shield, Sweden. The modeled ice sheet mimics the Weichselian ice sheet during its last major advance and retreat over northern Europe. The paper elaborates and analyzes different choices of top boundary conditions at the ice sheet-subsurface interface (e. g. ice-sheet thickness and ice-margin velocity) and in the proglacial area (presence or lack of permafrost) and relates these choices to available groundwater-flow-model hydraulic output and prevailing conceptual hydrogeochemical models of the salinity evolution at the two sites. It is concluded that the choice of boundary conditions has a strong impact on results and that the studied sites behave differently for identical boundary conditions due to differences in their structural-hydraulic properties.