Based on the multivariate joint probability distribution of the discharge and water quality indicators, this paper analysed the occurrence probabilities and improvement probabilities of combinations of water quality indicators under different discharge conditions and then presented a method for calculating the optimal discharge to seek a balance between the discharge dispatch and water quality improvement. The method was used to construct the relationship curve between the discharge and joint improvement probability used by a copula function and then calculate the critical point on the curve. The proposed method was applied to the Yi River Basin above Gegou Station with data composed of the discharge and main pollution indicators (NH3-N and CODMn) from 1982 to 2015. The results showed that the trivariate joint probability distribution can more reasonably reveal the statistical characteristics of different combinations of discharge and water quality indicators. Furthermore, the optimal discharges and the corresponding improvement probabilities that improved NH3-N and CODMn to different grades were calculated. The calculation method took the interdependence of multiple water quality indicators into account, thereby providing a more reasonable method for using discharge dispatch data to improve the river water quality.