The objective of this study was to investigate the relationship between the biomass of cyanobacteria and the concentration of 2-methylisoborneol (2-MIB) in the lower Gongji stream. The investigation was done using a field study that was conducted from 2015 to 2017. The 2-MIB concentration in the lower Gongji stream ranged from 0 to 153 ng/L, while the upper stream had 0 2-MIB concentration. 3 genera (Oscillatoria, Phormidium, Pseudanabaena) of cyanobacteria were detected in the lower Gongji stream with 2-MIB concentration. Among these 3 genera, an increase in Phormidium, Pseudanabaena biomass was associated with an increase in 2-MIB concentration. Accordingly, Phormidium, Pseudanabaena were regarded as the biological source of 2-MIB in that area. In October 2017, although planktonic cyanobacteria occurred less frequently, many benthic cyanobacteria mats were observed on the surface of the water body. Therefore, the high 2-MIB concentration, which exceeded 110 ng/L, can likely be attributed to the benthic cyanobacteria. In a laboratory experiment, individual Oscillatoria filaments were aggregated to form a colony with a higher density. This colony tended to float on the water surface. Cyanobacteria mats after floating aggregated mats were distributed in a net shape on the bottom.