Three sampling campaigns were carried out in rivers located at two hydrographic basins affected by urban and semi-urban areas around the Metropolitan area of A Coruña (ca. 500,000 inhabitants, NW-Spain) to study local and temporal variations of 21 physicochemical parameters (pH, conductivity, Cl-, SO4(2-), SiO2, Ca2+, Mg2+, Na+, K+, hardness, NO3(-), NO2(-), NH4(+), COD, PO4(3-), Zn2+, Cu2+, Mn2+, Pb2+, alkalinity and acidity) in 23 sampling points. The temporal evolution of the water quality was assessed by matrix augmentation principal components analysis (MA-PCA) and parallel factor analysis (PARAFAC). Moreover, classical principal components analysis (PCA) (one per sampling campaign) was applied with exploratory and comparison purposes. The first factor of the different studies comprised variables associated to the mineral content and it differentiated the samples according to their hydrographic basins. The second factor was mainly associated to organic matter, from domestic wastes and decomposition of natural debris. The temporal evolution of the water quality was mostly related to seasonal increments of the physicochemical parameters defining the decomposition of the organic matter. The three models applied (PCA, MA-PCA and PARAFAC) led to similar conclusions, nonetheless, MA-PCA excelled, since the refolding of scores provided more straightforward and convenient overview of sample time and geographical variations than individual PCA and it is more flexible and adaptable to environmental studies than PARAFAC.