A comprehensive eutrophication evaluation method was developed in this study to classify the eutrophication of main river estuaries in Taiwan into 5 ranks. In addition, MODIS satellite ocean color images were used to analyze the chlorophyll a concentrations in the estuarine and coastal waters. Integrated eutrophication evaluations were performed in three selected estuaries in the northern, central, and southern Taiwan and management strategies to mitigate eutrophication was consequently proposed. The results of the comprehensive evaluation indicated that the coastal areas of Taoyuan, Erren River Estuary, Gaoping River Estuary, and Dapeng Bay are currently the regions presenting the greatest eutrophication potential, and the overall water quality in these regions was ranked as Bad. The satellite ocean color images show that the estuaries of Jhuoshuei River, Puzih River, and Zengwun River, as well as 3 nautical miles off the coast, presented relatively high concentrations of chlorophyll (> 5μg/L). The evaluation results obtained from the ASSETS software further show that Danshuei River, Beigang River, and Gaoping River show significant symptoms of eutrophication, and were ranked as Poor to Bad.