The hydrogeological unit of Aguadulce (Campo de Dalías aquifers, SE Spain) has a complex geometry. This fact, together with a continuous rise in water demand due to intensive agriculture and tourism create problems for groundwater quantity and quality. In this paper classic geochemical tools managed by means of GIS software and geochemical simulations are combined to delineate, identify and locate the possible physicochemical processes acting in the Aguadulce groundwater. Two main aquifers can be distinguished: the carbonate or lower aquifer of Triassic age, and the calcodetritic or upper aquifer of Plio-Quaternary age. Groundwaters from the latter are more saline and, assuming all chlorinity originates from seawater intrusion, the seawater contribution to their composition would be up to 7%. Nevertheless the carbonate aquifer appears not to be homogeneous: it is compartmentalised into 4 zones where different processes explain the different groundwaters compositions. Zone 4 samples (E margin of the carbonate aquifer) resemble those of the Plio-Quaternary aquifer, where calcite precipitation, dolomite and gypsum dissolution and some cation exchange (water-rock interaction) together with seawater-freshwater mixing occur. In contrast, water-rock interaction predominates in zones 1 and 3 of the carbonate aquifer. Moreover, zone 2 samples, located between zones 1 and 3, are explained by water-rock interaction in addition to mixing with Plio-Quaternary aquifer waters. The combination of geochemical simulations with GIS and hydrogeochemical analyses has proven to be effective in identifying and locating the different physicochemical processes in the aquifer areas, thus improving understanding of hydrogeochemistry in complex aquifers. © 2012 Elsevier Ltd.