The current study analyzes the impact of physico-chemical and hydrological components on taxonomic diversity, density and Shannon’s diversity index for micro-benthic communities found in small lowland rivers. The purpose of this study was to determine major predictors among environmental factors that have an impact on benthic invertebrate communities dwelling in small rivers, and to compare the structure of the communities in terms of their abundance, biodiversity and abundance between the sites. For this purpose we studied a total of 30 sites located in 10 watercourses, where 95 taxa were identified, including 49 specific species. The study brought evidence of differences in the number of taxa, biodiversity indices and abundance of micro-benthic communities across specific sites. Ammonium ions, water velocity and phosphates were found to be major predictors among environmental factors having impact on benthic communities.