Due to the fact that public project governance with water resources balance sheet has to be carried out under the influence of multiple uncertain factors, under present conditions of water resources shortage, extensive water utilization management mode could hardly be continued any longer. Combining the provisions of China's water conservation policy in the new era and the deployment of water conservation competent organizations relating to specific work in constructing water ecological civilization, and abiding by objective developing law to establish feasible objective and have a scientific un derstanding the factor of system are essential requirements of public project governance based on water resources balance sheet. For this purpose, this paper associates project governance with water resources balance sheet, which carries out research by focusing on water ecological environment protection in public project governance, and devotes itself to developing public project governance system module based on water resources balance sheet. In addition, the paper keeps in line with the principle of adjusting measures in view of water and basing the demand on water resources to study the application objective of water resources balance sheet in public project governance, so that to strive to make the progress of social economy to accommodate water environment and water resources carrying capacity. The paper may provide experiences and references for public project governance objective setting, governance system factors control and public project governance approach at the request of ecological civilization construction.