The alluvial aquifer of the Guadalquivir River comprises shallow Quaternary deposits located in the central-eastern part of the Province of Jaén in southern Spain, where groundwater resources are used mainly for crop irrigation in an important agricultural area. In order to establish the baseline hydrochemical conditions and processes determining the groundwater quality, groundwater and river water samples were collected as part of an integrated investigation that coupled multivariate statistical analysis with hydrochemical methods to identify and interpret the groundwater chemistry of the aquifer system. Three main hydrochemical types (Mg-Ca-HCO3, Ca-Mg-SO4-HCO3-Cl and Na-Ca-Mg-Cl-SO4) were identified. Further interpretation, using R-mode principal components analysis (PCA) conducted with 13 hydrochemical variables, identified two principal components which explain 2/3 of the variance in the original data. In combination with the hydrochemical interpretation, mineralogical analyses of the aquifer sediment together with inverse geochemical modelling using NETPATH showed that dedolomitization (calcite precipitation and dolomite dissolution driven by gypsum dissolution) is the principal hydrochemical process controlling the regional groundwater chemistry. Other processes such as silicate weathering, ion exchange, mixing between river water and groundwater, and agricultural practices also affect the groundwater chemistry.