Improving the understanding and influence of small (metric) scale geological features in groundwater flow has been object of interest in the hydrogeological community for decades. In coastal aquifers, geological features such as fractures, sedimentary structures, karstification or presence of dykes, strongly determine the distribution and patterns of saltwater intrusion. Geophysical techniques have been largely utilized in coastal environment and provide large datasets with various resolutions that can be utilized to build and parametrize groundwater models. Here we present an integrated hydrogeophysical study conducted in a coastal site near Belfast, in Northern Ireland. In this area, the presence of volcanic dykes of metric thickness act like low permeability barriers affecting and controlling groundwater flow and saltwater intrusion patterns. To improve the understanding of the system a detailed geophysical survey including electrical resistivity tomography and magnetics has been performed. Modelling of magnetic data provides information about the spatial distribution and geometry of the volcanic dykes. Three-dimensional inversion of electrical data shows a compartmentalization of the groundwater system and the strong influence of the dykes in the spatial distribution of saltwater. All the information is finally integrated in a hydrogeophysical model implemented in a coupled numerical framework using a single code. The approach allows for simultaneous solving of the multiphysical problem. Modelled three-dimensional hydrogeophysical response is compared with observed data. The results significantly improve the resolution of the effect of dykes on groundwater flow as compared to previous independent approaches and clearly show the strong influence of local scale structures in saltwater intrusion.