Effective joint management of water quantity and quality of rivers requires a good understanding of the interrelationships between these variables. This study aims to quantitatively evaluate the impact of river streamflow on the joint occurrence of water quality variables in the heavily polluted Huai River Basin (HRB). Using data from three representative stations, joint distributions were set up for two key water quality indexes, CODMn and NH3-N, for three different streamflow scenarios: low, medium and high streamflows, and the joint probabilities of different water quality combinations were calculated. The results showed that there was a significant negative relationship between streamflow and the water quality index, while the water quality indexes were significantly positively correlated. In general, the higher the river streamflow, the lower the joint probability of water quality variables under the three scenarios in each station. It is concluded that, in both the main stream and the tributary, high streamflow scenarios do help to improve the joint probability of water quality combination under a higher water quality grade, compared with a decrease under a lower quality grade. This study is expected to provide scientific references for water quality management and implementation of water pollution prevention in the HRB.