Identification of the main contamination sources of heavy metals, organic compounds and other physicochemical parameters in Ebro river surface waters and description of their temporal and spatial distributions, are analyzed using chemometrics and geostatistical methods. Historical data available from the Confederación Hidrográfica del Ebro (CHE), which is the organization in charge of the management of the Ebro river basin; covering different years since 1992 for water, sediments and fish samples are investigated. Due to the great amount of data in these databases and to their complexity, chemometrics modelling (using principal components analysis, PCA) coupled to geographical information systems (GIS) is proposed to evaluate the environmental quality of the Ebro river basin.