This paper analyzes water quality from four hydrological stations in the Nišava river basin from 2009–2018 based on the following parameters: pH, conductivity, O2 saturation, BOD5, suspended solids, total oxidized nitrogen, phosphates, turbidity and coliform bacteria. Authors have applied WQI (water quality index) as the most reliable indicator of the watercourses pollution for setting of surface water flow quality. Statistical analysis of variance (ANOVA) using t-test inferential statistical analysis and post-hoc Tukey test were applied to evaluate statistically significant differences between specific data groups. The results show that bad water quality was registered on all the profiles on an annual basis (WQI = 65–71). The river water pH decreases downstream, while values of BOD5, suspended solids, turbidity, TON, phosphates and coliform bacteria gradually increase. The waters of the Nišava at the station Niš belong to the third class of waters and they are mostly loaded with organic matter originating from waste sewage and industrial waters of both urban and rural areas.