In highly heterogeneous aquifer systems, conceptualization of regional groundwater flow models frequently results in the generalization or negligence of aquifer heterogeneities, both of which may result in erroneous model outputs. The calculation of equivalence related to hydrogeological parameters and applied to upscaling provides a means of accounting for measurement scale information but at regional scale. In this study, the Permo-Triassic Lagan Valley strategic aquifer in Northern Ireland is observed to be heterogeneous, if not discontinuous, due to subvertical trending low-permeability Tertiary dolerite dykes. Interpretation of ground and aerial magnetic surveys produces a deterministic solution to dyke locations. By measuring relative permeabilities of both the dykes and the sedimentary host rock, equivalent directional permeabilities, that determine anisotropy calculated as a function of dyke density, are obtained. This provides parameters for larger scale equivalent blocks, which can be directly imported to numerical groundwater flow models. Different conceptual models with different degrees of upscaling are numerically tested and results compared to regional flow observations. Simulation results show that the upscaled permeabilities from geophysical data allow one to properly account for the observed spatial variations of groundwater flow, without requiring artificial distribution of aquifer properties. It is also found that an intermediate degree of upscaling, between accounting for mapped field-scale dykes and accounting for one regional anisotropy value (maximum upscaling) provides results the closest to the observations at the regional scale.