The evaluation of water quality usually considers the effect of different physical and chemical parameters, which can vary across space and time. In this context, it is crucial to build a spatio-temporal composite indicator which might provide useful insights for a sustainable development and might support strategies for saving water and controlling pollution. For this aim, an advanced Geographically weighted principal components analysis indexed in time, based on the use of geostatistical tools, is proposed. Thus, this technique is applied on parameters observed for ten years, for the superficial rivers of Emilia-Romagna Region, which presents a complex water system.