The aqueous environment quality plays an important role in controlling the circulation track of ecological environment. Environmental isotopes widely exist in various kinds of water and can be extensively applied in water environment. Isotopes as natural tracers can be used to trace the transportation process of water in hydrologic cycle and the variations of isotopic value can also provide the information about the transference of contamination. The dynamical process of the movement and mix of waters can be studied by applying the composition characteristics of stable isotopes contained in natural waters, thus the main processes of water resources formation and aqueous environment evolution as well as their driving forces mechanism can be revealed. In this paper, the development history of the application of stable isotopes in the water circulation is reviewed, the application theory and analytical method of the environmental stable isotopes, and the new progress of the applied study on water resources formation and aqueous environment evolution are mainly discussed.