During the fall and winter of 1995, ninety-two samples were collected from twenty-three sampling stations in the Matanza-Riachuelo river basin. Epipelic diatoms and physico-chemical parameters were studied to establish water quality. Ecological methodologies (species richness, diversity and saprobity indices and multivariate analysis) were employed to assess the impact of the pollution on diatom assemblages. Suspended solids, biological and chemical oxygen demands increased downstream, and dissolved oxygen, pH and transparency increased upstream. Conductivity was variable. This fluvial system is affected by organic and inorganic pollutants, many of them toxic. The presence of heavy metals, phenols, pesticides, hydrocarbons among other chemicals, mostly account for the impoverishment of the diatom assemblages of the basin, thus leading to changes in assemblages structure. Changes in water quality were better reflected by species richness, diversity indices and by principal component analysis than pollution indices in this basin.