The support mechanism of scientific and technological innovation for the construction of water ecological civilization is analyzed. It is systematically discussed from three aspects, that is, demand, condition and conduction path of the construction of water ecological civilization supported by the scientific and technological innovation. The results show that the support of fundamental science innovation, applied technology and method innovation, and scientific and technological practice innovation is necessary to the construction of water ecological civilization. The play of this support needs the premise of ecological science and technology, the internal motives such as interest driving, entrepreneurs’ innovation spirit and internal system as well as the external motives like demanddriving force, police-driving force, social cooperation, legal safeguard and cultural leading force. The support conduction paths include the soft power improvement of construction of water ecological civilization, the allocation optimization of water resources, the water saving management and the protection of water ecological environment.