Groundwater pathways and residence times are controlled by aquifer flow and storage properties, which, in weathered/fractured hard rock aquifers, are characterized by high spatial heterogeneity. Building on earlier work in a metamorphic aquifer in NW Ireland, new clay mineralogy and analyses of geophysical data provided high spatial resolution constraints on the variations in aquifer properties. Groundwater storage values derived from magnetic resonance sounding and electrical resistivity tomography were found to largely vary laterally and with depth, by orders of magnitude. The subsequent implementation of hillslope, two-dimensional numerical groundwater models showed that incorporating heterogeneity from geophysical data in model parametrization led to the best fit to observations compared with a reference model based on borehole data alone. Model simulations further revealed that (1) strong spatial heterogeneity produces deeper, longer groundwater flow paths and higher age mixing, in agreement with the mixed sub-modern/modern ages (mostly <50 years) provided by independent tritium data, and (2) areas with extensive weathering/fracturing are correlated with seepage zones of older groundwater resulting from changes in the flow directions and are likely to act as drainage structures for younger groundwater on a catchment or regional scale. Implications for groundwater resilience to climate extremes and surface pollution are discussed together with recommendations for further research.