Classification of estuarine and coastal waters has been recognized as a critical step for natural resource managers to describe and inventory coastal systems, understand constraints, predict the most sensitive systems, manage and protect coastal resources. However, the research on ecological classification in China is still in infancy, especially the classification of estuarine and coastal waters at regional or nationwide scale. This research employed Geographical Information System (GIS) and multivariate statistical analyses to delineate and classify the watersheds and estuarine drainage areas from fifteen major coastal rivers in China. The Hydrology module in ArcGIS environment was used to delineate the sub-watersheds from the fifteen coastal rivers, represented by spatially different details with five thresholds. The watershed boundaries of fifteen coastal rivers were further delimited and validated with literature documents. The deviation was less than 10%. Based on the analysis of spatial distribution of tide heads for fifteen rivers and the previously delineated sub-watersheds, 88 estuarine drainage areas (EDAs) were further defined. A five-class classification system was developed with the hierarchical cluster analysis, based on the physical, biological and chemical properties of EDA. Estuaries having the smallest total EDA were grouped as class one, and they are located in Bohai Bay, Shandong peninsula and coastal areas of Guangdong; estuaries having the lowest average salinity range and the highest concentration of total suspended solid were grouped as class two, and they are located in Yangtze River estuary and Hangzhou bay; estuaries having the highest average depth and the highest wind speed were grouped as class three, and they are located in coastal areas of Northern Jiangsu and Liaodong peninsula; estuaries having the lowest dissolved oxygen and highest tidal range were grouped as class four, and they are located in coastal areas between Shandong and Jiangsu, coastal areas of Southern Jiangsu; estuaries having the largest average EDA and highest freshwater flow were grouped as class five, and they are located in coastal areas of Fujian and Zhejiang, Pearl river estuary, Haihe River estuary, and Liaohe River estuary. A rapid bio-assessment procedure was successfully employed to validate the classified result based on the collected data from literatures. The findings in this study provided the basic geospatial data for further developing nutrient criteria and eco-regionalization in estuarine and coastal waters in China.