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The Sava River Basin is a major drainage basin of southeastern Europe, significantly influenced by anthropogenic activities. Our study was focused on diatom communities as an indicator of the ecological status of running waters. We investigated over 937 km of the Sava River at 19 sampling sites. Benthic diatom communities and 17 diatom indices were analyzed along with a large set of environmental parameters. CCA revealed that the most important elements along the spatial gradient were As and Si. Our results show that the species Navicula recens (Lange-Bert.) Lange-Bertalot and Eolimna minima (Grunow) Lange-Bertalot are very abundant at downstream localities where the highest concentrations of As were measured. The number of motile diatoms increased along the nutrient gradient, i.e. with Si availability. Correlations between diatom indices and selected environmental factors showed that temperature, As, Si and Fe are in significant negative correlation with most diatom indices. Analysis revealed the influence of As and metals in water on diatoms, although their concentrations did not exceed environmental standards. While our findings do not confirm that diatom indices reveal the intensity of pressures solely caused by nutrient and/or organic pollutants, they suggest that in moderately polluted large rivers benthic diatoms are good bioindicators of multiple pressures, and that diatom indices could serve as indicators of the level of overall degradation of an ecosystem. [ABSTRACT FROM AUTHOR]