There are regular problems of musty odor in the Huangpu River, a major source of drinking water for Shanghai, China. In this study, the musty odor and its main causative compounds in the Huangpu River source water were confirmed through a yearly investigation using flavor profile analysis combined with HSPME-GC-MS analysis. The investigation showed that 2-methylisoborneol (2-MIB) with a concentration level between 28.6 and 71.0 ng/L was responsible for the musty odor in summer from July to September. Microscopic observation confirmed with the cloning results showed that Phormidium spp., which accounted for 80%-95% of the algal cell density, was the microorganisms responsible for the production of 2-MIB and the estimated 2-MIB yield was 0.022 pg/cell. Results from a wide-area sampling campaign in the Huangpu River watershed showed that, other than the large tributaries receiving water from Tai Lake, several small creeks close to the intake may have contributed most of the 2-MIB and the Phormidium spp. to the Huangpu River source water. This study provides methodology for the investigation of odor causing compounds and microorganisms in river-type source water, and the result will be useful for water quality control in both source water and drinking water.