Benthic macroinvertebrates are used to evaluate water quality in 8 sampling stations in Lepenci river basin in Kosovo. Sampling was performed in spring, summer and fall 2017. Following biotic indices are used: EPT taxa richness, Biological Monitoring Working Party (BMWP), Average Score per Taxon (ASPT), Stroud Water Research Center index (SWRC), Family biotic index (FBI), as well as diversity indices: Shannon-Weaver index (H), Simpsons index (D), Hill’s index (Hi), Mergalef index (DMe) and Menhicnik’s index (DMa). Our results show the presence of 34 macroinvertebrate taxa in Lepenci river which belong to Insecta, Crustaceans and Annelidae. The water quality along the river show variation from high and good class upstream, to moderate, poor and bad, downstream. The Pearson’s bivariate correlation used to analyze the relationship between physicochemical parameters with biotic and diversity indices showed a significant correlation (p < 0.01) of EC, TSS, O2, COD, BOD, NH4, and PO43- with biotic indices EPT, BMWP, ASPT, SWRC, FBI. We can conclude that the values of biotic and diversity indices have shown differences in water quality between polluted and unpolluted sites and reflect the ecological status of the river, therefore we can consider them as valuable tools for water quality assessment in rivers in Kosovo.