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This study was undertaken to investigate the distribution and variation of microcystins (MC) from a water resource to a water plant in China including long distance transportation, ClO2 preoxidation, coagulation/precipitation, filtration, and disinfection. Advanced treatment methods including ozonation and granular activated carbon (GAC) adsorption were tested to remove microcystins from drinking water. The results indicated that, when containing high level of algae in raw water, preoxidation at 2 mg/L of ClO2 was not enough to stop algae growth in long distance transportation. In the water plant studied, both coagulation and filtration caused significant increase instead of removal of microcystins in drinking water. Chlorine disinfection removed part of microcystins. However, both ozonation and GAC adsorption were able to remove microcystins completely, thereby improving the quality of drinking water in terms of microcystins.