长江水环境保护是维持长江健康生命的关键。针对由于水环境问题而引起的长江“亚健康”现状，从流域系统观出发，基于流域系统的演化“山-河-湖-海互动理论”，从多学科综合研究的角度，提出了长江水环境问题在基础研究、应用研究和目标研究3个层次的研究思路，重点对人类活动和全球变化作用下长江流域山-河-湖-海相互作用及流域水环境演化规律、重大水环境问题的成因机理、流域水环境的承载能力及调控原理的研究内容和研究途径进行了论述。旨在引起人们对长江水环境问题研究的关注，推动长江水环境问题研究的开展，为新时期的治江战略制定服务。

Water environment protection is a key to maintain the Yangtze River’s exuberance. The research thought on the Yangtze River water environment at three stratifications, namely basic research, applied research and aim research, is represented? on the basis of the sub-healthy situation of the Yangtze River,? the view-point of multidisciplinary synthesis and the theory of mountain-river-lake-sea affiliation from the evolution of the river basin system. The emphases are to discuss about the research contents and approaches of some critical problems including the interactive mechanism of mountain-river-lake-sea, rule of the water environment ?evolution, formation of big water environment problems, carrying capacity and controlling elements of the water environment under the effect of human activities and global change. This article aim is to cause people’s attention to the Yangtze River water environment to impulse the research and help constitute the stratagem of new-time river management.