Saltwater intrusion is generally related to seawater-level rise or induced intrusion due to excessive groundwater extraction in coastal aquifers. However, the hydrogeological heterogeneity of the subsurface plays an important role in (non-)intrusion as well. Local hydrogeological conditions for recharge and saltwater intrusion are studied in a coastal groundwater system in Vietnam where geological formations exhibit highly heterogeneous lithologies. A three-dimensional (3D) hydrostratigraphical solid model of the study area is constructed by way of a recursive classification procedure. The procedure includes a cluster analysis which uses as parameters geological formation, lithological composition, distribution depth and thickness of each lithologically distinctive drilling interval of 47 boreholes, to distinguish and map well-log intervals of similar lithological properties in different geological formations. A 3D hydrostratigraphical fence diagram is then generated from the constructed solid model and is used as a tool to evaluate recharge paths and saltwater intrusion to the groundwater system. Groundwater level and chemistry, and geophysical direct current (DC) resistivity measurements, are used to support the hydrostratigraphical model. Results of this research contribute to the explanation of why the aquifer system of the study area is almost uninfluenced by saltwater intrusion, which is otherwise relatively common in coastal aquifers of Vietnam.