Abstract: The classification and segmentation of water bodies form the premise and basis for determining estuarine and coastal nutrient criteria, which is critical to the development of precise and differentiated estuarine nutrient control as well as water quality assessment in land-sea integration in China. Here, the research progress of classification and segmentation of estuarine offshore water bodies in the United States, the European Union and China was summarized, and the representative methodologies were introduced combined with typical cases. Key classification and segmentation factors (i.e., topography and geomorphology, salinity, bathymetry, hydrodynamic factors, and substrate) were investigated for their ecological relevance. On the basis of current studies and the characteristics of China’s estuarine and coastal ecological environment, a preliminary framework for classification and segmentation of estuarine and coastal waters in China was proposed in terms of overall thoughts, classification of water body types and factor selection. Our review provides important basis for determining and revising nutrient criteria and standards, as well as for managing the ecosystems in estuarine and coastal waters.