The new project management principle of implementing the total control in large, interdisciplinary, cross-industries and cross-regions systems to promote the transformation of the economic development way in the adjustment of industrial structure and the drive of science and technology innovation etc. was presented and discussed. Using three red lines of water resource exploitation, utilization and protection decided in the Central Water Conservancy Working Conference and the project planning which the author chaired or participated in Beijing and Shanghai as the case, the quantitative analysis on the total control of the water environment and resources engineering was made, which can be referenced by all types of the total project control.