The water quality and river discharges were surveyed at two sites in Nišava River basin (Dimitrovgrad and Niš) with complete data series for the ten-year period (2005)(2006)(2007)(2008)(2009)(2010)(2011)(2012)(2013)(2014). For these stations SWQI was calculated and correlation analysis was applied. The index value is dimensionless and varies between 0 and 100 (best quality) It is derived from numerous physical, chemical, biological and microbiological parameters. At Niš station average annual value of SWQI is 78 (good) with a clear decrease trend over a ten-year period. On the other side, on Dimitrovgrad station, average annual SWQI is 89 (very good) with a clear positive trend. Goal of this paper was to determine if there is a correlation between river discharge and values of SWQI. Results of the Pearson correlation test between SWQI and daily discharge values for Dimitrovgrad station show a moderate linear relation was observed, r= -0.287, p = 0.002. On Niš station same test has shown that there is no statistically significant relation between discharge and water quality (r=0.103 p= 0.297). This study has shown that the correlation between SWQI and discharge is weak or not present at all at the investigated river.