This study simulates and quantifies the exchange and the pathways of deep and shallow groundwater flow and solute transport under different climate and permafrost conditions, considering the example field case of the coastal Forsmark catchment in Sweden. A number of simulation scenarios for different climate and permafrost condition combinations have been performed with the three-dimensional groundwater flow and transport model MIKE SHE. Results show generally decreasing vertical groundwater flow with depth, and smaller vertical flow under permafrost conditions than under unfrozen conditions. Also the overall pattern of both the vertical and the horizontal groundwater flow, and the water exchange between the deep and shallow groundwater systems, change dramatically in the presence of permafrost relative to unfrozen conditions. However, although the vertical groundwater flow decreases significantly in the presence of permafrost, there is still an exchange of water between the unfrozen groundwater system below the permafrost and the shallow groundwater in the active layer, via taliks. ‘Through taliks’ tend to prevail in areas that constitute groundwater discharge zones under unfrozen conditions, which then mostly shift to net recharge zones (through taliks with net downward flow) under permafrost conditions.