Aquatic ecoregion, as one type of ecoregions, is a unit of land of relative homogeneity in aquatic ecosystems or in relationships between organisms and their environments. It is the base of establishing the trophic state standard for the lakes and reservoirs, and that of controlling the eutrophication. In this paper, we put forward the principles and assessment index of trophic state divisions for the lakes and reservoirs in China. Based on the assessment index and with the help of spatial analysis of geographic information system, expert judgment and qualitative analysis, we suggest that all the lakes and reservoirs in China be divided into three Level I and six Level II ecoregion divisions. Moreover, the trophic state characteristics of each ecoregion division are summarized.