The equitable allocation of water governance responsibilities is very important yet difficult to achieve, particularly for a basin which involves many stakeholders and policymakers. In this study, the environmental Gini coefficient model was applied to evaluate the inequality of water governance responsibility allocation, and an environmental Gini coefficient optimisation model was built to achieve an optimal adjustment. To illustrate the application of the environmental Gini coefficient, the heavily polluted transboundary Taihu Lake Basin in China, was chosen as a case study. The results show that the original environmental Gini coefficient of the chemical oxygen demand (COD) was greater than 0.2, indicating that the allocation of water governance responsibilities in Taihu Lake Basin was unequal. Of seven decision-making units, three were found to be inequality factors and were adjusted to reduce the water pollutant emissions and to increase the water governance inputs. After the adjustment, the environmental Gini coefficient of the COD was less than 0.2 and the reduction rate was 27.63%. The adjustment process provides clear guidance for policymakers to develop appropriate policies and improve the equality of water governance responsibility allocation.