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We analyzed the following characteristics of water self-depuration capacity along a polluted river (Suquía River) in Argentina: a) abundance of microbial metabolic groups, b) cover and type of vegetation, and c) type and concentration of soil and sediment humic substances. The objective was to establish the modifications of water self-depuration characteristics of the polluted sites in comparison to a reference site, in order to provide basic data for ecological restoration programs. Five samples of riparian soil, water and sediments were collected at a reference site and five polluted sites during low and high flow water periods. In each site the vegetation type and soil cover were recorded. In all samples the abundance of ammonifiers, nitrate-reducers, sulfate-reducers, cellulolytic microorganisms, aerobic heterotrophs and fermenters were measured. Besides soil and sediment organic matter and humic and fulvic acids content were analyzed. Our results showed that all sites differed in their water self-depuration characteristics with respect to the reference site and that these variations are due to a combination of natural and anthropic factors. The Suquía River presents a great heterogeneity of water self-depuration characteristics but it does not achieve a mitigation of the anthropogenic impact produced by Córdoba city. We concluded that restoration actions in lotic ecosystems should be adapted for each river sector.