Volcanic dykes are common discrete heterogeneities in aquifers; however, there is a lack of field examples of, and methodologies for, comprehensive in situ characterization of their properties with respect to groundwater flow and solute transport. We have applied an integrated multiphysics approach to quantify the effect of dolerite dykes on saltwater intrusion in a coastal sandstone aquifer. The approach involved ground geophysical imaging (passive magnetics and electrical resistivity tomography), well hydraulic testing, and tidal propagation analysis, which provided constraints on the geometry of the dyke network, the subsurface saltwater distribution, and the sandstone hydrodynamic properties and connectivity. A three-dimensional variable-density groundwater model coupled with a resistivity model was further calibrated using groundwater and geophysical observations. A good agreement of model simulations with tide-induced head fluctuations, geophysically derived pore water salinities, and measured apparent resistivities was obtained when dykes' hydraulic conductivity, storativity, and effective porosity are respectively about 3, 1, and 1 orders of magnitude lower than the host aquifer. The presence of the dykes results in barrier-like alterations of groundwater flow and saltwater intrusion. Preferential flow paths occur parallel to observed dyke orientations. Freshwater inflows from upland recharge areas concentrate on the land-facing side of the dykes and saltwater penetration is higher on their sea-facing side. This has major implications for managing groundwater resources in dyke-intruded aquifers, including in coastal and island regions and provides wider insights on preferential pathways of groundwater flow and transport in highly heterogeneous aquifer systems.