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Paldang Lake in the Han River system is an important source for supplying drinking water. Recently, the occurrence of odor compounds geosmin and 2-methylisoborneol (2-MIB), in Lake Paldang has adversely affected the drinking water supply. The causative organisms of odor compounds have not been identified. Thus, this study analyzed the correlation between odor compounds and microorganisms and identified the odor-producing microorganisms in the Han River system. Odor compounds were primarily detected in the Bukhan River system but not in the Namhan River system. Geosmin was detected at high concentrations in summer, whereas 2-MIB was detected at high concentrations in summer and autumn. Microorganisms that appeared at the time of geosmin occurrence were actinobacteria (0.317, p < 0.01) and Dolichospermum (0.326, p < 0.01) among cyanobacteria, and the correlation was significant. The occurrence of 2-MIB mainly coincided with actinobacteria (0.745, p < 0.01) and Pseudanabaena (0.321, p < 0.01) among cyanobacteria, and the correlation was significant. Therefore, to manage the odor compounds in Lake Paldang, which is a drinking water source, it is important to control the appearance of actinobacteria and cyanobacteria in the Bukhan River system. HIGHLIGHTS The generation of odor substances in Paldang Lake, the source of drinking water, was greatly influenced by the Bukhan River.; Geosmin positively correlated with Dolichopermum and Actinobacteria.; 2-MIB positively correlated with Pseudanabaena and Actinobacteria.; For the management of odor compounds in Lake Paldang, the drinking water source, it is important to identify the appearance of cyanobacteria and actinomycetes.;