This study presents a novel approach for the hydrogeological assessment of sedimentary coastal aquifers. Specifically, the methodology is tailored for modeling groundwater flow and nitrates contamination in typicalMediterranean coastal plains with high anthropogenic pressures, as exemplified by the Arborea plain (central western Sardinia, Italy). The study started with development of an updated geological–depositional model based on sequential stratigraphy. Geological and geophysical data, processed in a geographic information system (GIS) environment, supported the definition of a 3D hydrogeological conceptual model and provided a solid basis for the interpretation of groundwater flow directions. The 3D hydrogeological model allowed constraining groundwater circulation, flow paths and distribution of nitrate concentrations in the aquifers. The methodology appears as a valid tool applicable in other coastal areas to determine geological and hydrogeological settings. The definition of a quantitative hydrogeological framework will support the effective management of local water resources.