A river water quality management model under average climatic conditions may not be able to account for the extreme risk of low water quality which is more prominent under an increase in river water temperature and altered river flows. A modeling framework is developed to assess the risk of river low water quality extremes by integrating a statistical downscaling model based on Canonical Correlation Analysis, risk quantification model based on Frank Archimedean Copula function and multiple logistic regression model integrated with a river water quality simulation model, QUAL2 K. The results reveal that the combination of predicted decrease in low flows of approximately 57% and increase in maximum river water temperatures of approximately 1.2°C has shown an increase of about 46% in risk of low water quality conditions for the future scenarios along Tunga-Bhadra River, India. The extreme risk of low water quality is observed to increase by 50.6% for the period 2020–2040 when compared with the current extreme conditions of 4.5% and average risk conditions of about 3% for the period 1988–2005. The study captured the occurrence of extremes of low water quality with evidence of a strong link between climate and water quality impairment events.