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Heterogeneity of natural systems governs the pathway of pollutants in the environment, especially in aquifers. The relationship between a number of environmental pressures and the complex structure of groundwater flow systems generates many processes, which affect the behaviour and transport of pollutants. With regard to the wide variety of structural, volcanic and depositional processes which characterize the alluvial aquifer systems in the Campania Region (South Italy), this paper describes an integrated approach to delineate aquifer/aquitard units and recognize scale-dependent heterogeneity by means of geological, hydrogeological, geochemical and geostatistical techniques. In this analysis, a set of indicators, representative of the groundwater composition, have to be defined. Each indicator describes a specific aspect of groundwater quality and leads in combination with others to the definition of groundwater environmental index, due to natural and anthropogenic phenomena. The results of multivariate statistical analyses provide the identification of a number of homogeneous zones even in complex alluvial aquifer systems. At the same time, in wide regions this analysis enables to point out the most vulnerable sites and leads the working scale for planning technical and procedural solutions.