Under the constraint of water environmental carrying capacity, it is effective and insightful to control wastewater discharge and allocate water pollutant discharge permits for each pollution sources (or watershed control units) targeting at alleviating the pressure of water contamination. With a case study of Qinhuai river basin of Nanjing, China, water environmental capacity and top-down mandatory pollutants discharge reduction management were incorporated into water pollutant discharge permits decision system. In this study, a weighted multi-criteria environmental Gini coefficient method consisting of social (population), economic (gross value of industrial output), environmental (water environmental carrying capacity) and natural (land area) concerns was proposed to allocate the water pollutant discharge total phosphorus (TP) and NH3–N permits. Subsequently, based on the dual goals of minimum ECG under the constraint of water environmental carrying capacity and the limits of pollutants discharge reduction rate, the current discharge distribution, discharge permits distribution and discharge reduction distribution after allocation optimization of TP and NH3–N were obtained. The results showed that: (1) The water pollutant discharge (TP and NH3–N) permits exert a patchy configuration, and most of the watershed control units were suggested to reduce the emission by 60%. (2) After optimization, the Gini coefficients for NH3–N were lower, while the Gini coefficients for TP were increased slightly. (3) The total Gini coefficient for TP and NH3–N were all below 0.2, illustrating the water pollutant discharge permits are equity. The study shall be helpful to the policymakers to formulate total mass of pollutants control in environmental management and provide reference of further implementation of pollutant discharge permits trading system.