During the study on the assessment of ecological status of the Lepenci river basin, epilithic diatoms were used. Via this methodology, the authors aimed to standardization the ecological assessment methodology and gradually make it applicable for all river basins of Kosovo. The authors relied on a hypothesis that the epilithic diatom communities can serve as a reliable ecological tool to evaluate the quality of flowing waters in Kosovo. Thirteen water quality indices (IBD, IPS, IDG, DESCY, SLA, IDSE, IDAP, EPID, CEE, WAT, TDI, IDP and SHE) were measured in eight sample-points. From the conducted qualitative analysis, the obtained results showed that the water quality varies from upper parts of the basin (SP1, SP2, SP3 & SP4) characterized with higher water quality towards the lower parts (SP5, SP6 & SP7) where water quality was of the 2nd class and finally in Hani i Elezit (SP8) where the index values showed that its water belongs to the 3rd class. The samples were taken in to 8 sampling sites, in river during year (2017), the Navicula viridula species was the most dominant, along with Cocconeis placentula var. lineate and Diatoma vulgaris. In turn, between August and end of September, the following species were dominant ones: Craticula ambigua, Navicula hintzii, Navicula viridula and Rhoicosphenia abbreviata.