River health assessment is an essential and effective approach to river control. Historical understandings on river health especially on urban rivers are analyzed. The characteristics of mountainous urban rivers on hydrology, morphology, runoff, pollution, ecological services and anthropogenic impacts are analyzed based on a branch of the Yangtze River in Chongqing City. The watersheds including the river, its landscape and human actions are thought to be a suitable study unit, and mountainous urban river health should be of the following four meanings: internal ecological integrity, elasticity and recoverability of the river system itself, security of spatial landscape pattern of watershed, harmoniousness between the river system and urban people, and the sustainability over time of the abovementioned attributes. An indicator system was proposed for the assessment of mountainous urban river health. Analysis of spatial landscape pattern assisted with GIS tools should be emphasized as an indispensable part. 