To better understand the river chief system and to promote its smooth implementation so as to improve the utility level of river and lake governance, the applicability and practicability of the river chief system are demonstrated by using the holistic governance theory. The general situation and progress as well as the problems in the actual implementation of the river chief system are analyzed, such as responsibility vacuum in the implementation of hierarchic integration, difficult sustainability in the pressure orientation of functional integration, individualization in the participation subjects of department integration. In view of these problems, some suggestions are put forward: construction of overall responsibility, design of legal guarantee system and advocation of multiple participation subjects.