According to analysis of the evolution of the river courses, this paper presented the environment changes in the lower reaches of Heihe River approximately. As the common scenes in arid areas in Northwestern China, the environment changes caused by the processes of water system shrinking with tracing to the sources mainly because of the tectonic movement and climate changes in the geologic historical times. The processes were accelerated by the unreasonable development of water and land resources during recent 2,000 years. Badain Jaran Desert were the lower reaches of Heihe River. The Ejina Delta would be Ejina Desert if the Ejina Oasis disappeared as the processes of Badan Jaran Desert formation. In the early Pleistocene, there were two water systems in Ejina Region with the warm and humid climate relatively. Afterwards, the two water systems combined one system with the drought climate. In the late Pleistocene, modern water system was formed as the climate was much more drought. The Juyan Lakes were not the terminal lakes of Heihe River but were river channel lakes in the geological period. They pxperienced processes of reducing and disappearing as the water system shrinking of Heihe River courses, therefore, were terminal lakes in modern times with an ephemeral period obviously.