In urban rivers in many fast-growing cities, heavy metals pollution is one of the major quality issues. Quantifying its recovery success seems to be a difficult but necessary challenge, in part, because a complex database is generally needed to assess water quality. The overall goal of this work was to evaluate temporal changes in metal concentrations in a polluted basin applying the AEM method and to determine the physicochemical and meteorological parameters associated with these changes using the RDA. We analyzed temporal changes of 15 sites located in the Matanza Riachuelo River Basin, one of the most polluted basins in the word. For this, we collected data of metal concentrations in surface water, physicochemical parameters of water and meteorological factors of eight years (2008 to 2015) in each site. The results of this work allowed make evident temporal patterns (at different scales) in metal concentrations and several factors associated with these patterns. Also, we found that the effects of physicochemical and meteorological factors in metal concentrations were dependent of each site, possibly related to the presence of different sources of pollution or characteristics of the river. Our study showed that the combination of AEM and RDA multivariate techniques is a useful tool for both detecting temporal trends in the concentrations of environmental pollutants, which are not easily detectable in highly degraded environments, and for evaluating factors associated with these changes. These techniques could be applied to different scenarios (aquatic and terrestrial) affected by the continuous advance of human activities.