Based on the connotations of river and lake health and the management system of regionalization of major water functions in China, the relationship between health assessment of rivers and lakes and water function regionalization are analyzed in this paper. The connotations of river and lake health based on water function regionalization are discussed. The characteristics of health rivers and lakes are proposed and the assessment principles are expounded. It is pointed out that the river and lake health assessment based on water function regionalization should refer to the characteristics of different water function areas and the leading function of water body type, in order to determine the focus of the assessment first, and then determine the weights and the assessment indices for different water function areas. Meanwhile, the assessment indices should reflect the characteristics of health rivers and lakes, and thus the health status of the rivers and lakes could be evaluated comprehensively.