Consumers generally concern taste and odor in drinking water. In the Southern Taiwan, more than 5,000,000 people are suffered from earth/musty odor in drinking water, especially in the summer. Thus, ozonation of geosmin (GSM), 2-methylisoborneol (2-MIB), and 2-furfural (2-FF) in eutrophic surface waters has been studied in the present work. Experimentally, it was found that the water contained high dissolved organic carbon (DOC), humic substances, and specific ultraviolet absorbance (SUVA) resulting the highly ozone (O3) demand. The natural organic matters (NOM) in the waters had a significant effect on the ozonation of GSM, 2-MIB and 2-FF. Their destruction rates were increased with high contents of aromatics, phenolics, and SUVAs. In addition, during ozonation of raw waters, O3 and OH. played an important role in destruction of algae cells and caused excretion of extracellular organic matter (EOM) to the bulk phase.