In view of the multiple reaches,complex environments as well as intensive ecological sensitive areas and high social sensitivity in the second phase of the Yangtze River 12.5 m deepwater channel project below Nanjing,we analyze the possible influence of the project on the surrounding environment and clarify the main environmental problems.Through establishing the environmental protection work management organization and formulating the management principle of the environmental protection work,we carry out the whole process environmental protection management.The practice shows that remarkable progresses are achieved in the environmental protection work and the harmonious unification of project construction and ecological development is realized.