Freshwater biofilms can be useful indicators of water quality and offer the possibility to assess contaminant effects at the community level. The present field study examines the effect of chlor-alkali plant effluents on the community composition of biofilms grown in Olt River (Romania) reservoirs. The relationship between ambient water quality variables and community composition alterations was explored. Amplicon sequencing revealed a significant modification of the composition of microalgal, bacterial and fungal communities in the biofilms collected in the impacted reservoirs in comparison with those living in the uncontaminated control reservoir. The abundance corrected Simpson index showed lower richness and diversity in biofilms collected in the impacted reservoirs than in the control reservoir. Biofilm bacterial communities of the impacted reservoirs were characterized by the contaminant-tolerant Cyanobacteria and Bacteroidetes, whereas microalgal community were predominantly composed of Bacillariophyta and fungal communities of Lecanoromycetes and Paraglomycetes. A principal component analysis revealed that major contaminants present in the waste water of the chlor-alkali production plant, i.e. Na+, Ca2+, Cl- and Hg, were correlated with alteration of biofilm community composition in the impacted reservoirs. However, the biofilm composition was also influenced by water quality variables such as NO3-, SO42-, DOC and Zn from unknown sources. The results of the present study imply that, even when below the environmental quality standards, typical contaminants of chlor-alkali plant releases may affect biofilm composition and that their impacts on the microbial biodiversity might be currently overlooked.