Alongside history, human activities have contributed to the deployment of environmental quality. In particular, during the last decades the problem of water preservation has gained increasing attention.Statistical analysis is essential to analyze environmental data and to identify trends of pollutants over space and time. Usually applied techniques for data treatment are based on the organization of data in a two-way array, missing some shades on pollutants distribution. This fact supports the use of multi-way techniques, which allow the analysis of the results through different directions at the same time. For Three Modes Principal Components Analysis (3MPCA) a principal components analysis is conducted using three modes and a “core” matrix that allows assessing their interactions. In the case of environmental studies, it offers information about the spatial–temporal evolution of pollutants in a certain water body.The Guadalquivir River estuary has been used as a model system. It is a representative human influenced system, where different pollution inputs have been characterized. In this study, decadal evolution of pollutants has been discussed, to evaluate among others the effects of EU legislation on river water quality.The aim of this work is the establishment of the evolution, during the last decade, of nutrients and metals ultra-traces distribution in an estuary affected by anthropic activities. As examples, Pb and PO43− show a trend to decrease their weight on water pollution, total suspended solids (TSS) behavior is related with massive rain events, and the rising of new technologies appears as a source of emerging pollutants as Co in urban-industrial areas.