We analyzed cyanobacterial community including akinete, resting cell, and benthic cyanobacteria in sediment of Bukhan, Namhan-River, Paldang-Lake, and Kyeongan-Stream and compared the physicochemical factors for water and pore water. We also performed cyanobacteria growth potential test through incubating sediment. As a result of physicochemical analysis, the concentrations of nutrients were similar for each depth of Bukhan-River. For Namhan-River and Lake Paldang sites, the concentrations of TP and DTN in bottom and deep water had higher levels. DTN in water body composed of NO3-N(73%) while DTN in pore water composed of NH3-N(77.8%). Benthic cyanobacteria in the sediment such as Oscillatoria tenuis, O. limosa, Phormidium tenue, Pseudanabaena limnetica, and Lyngbya sp. were dominant (between 0.0~243.3×10 3 cells/g, w/w).Cell densities of cyanobacteria in sediment depth of 0~2 cm in most sites were higher compared to those in other depths. The cell density of cyanobacteria in sediment correlated with pH, conductivity, BOD5, TP, DTP, and chl. a. Increased phytoplankton and organic matters were found to be able to inhibit the growth of benthic cyanobacteria. Results of cyanobacteria growth potential test after incubating sediment revealed that harmful cyanobacteria (Anabaena, Aphanizomenon, Microcystis, and Oscillatoria) appeared at 7 days post culturing. Base on these results, the methods used in this study are considered to be able to determine the appearance of harmful cyanobacteria.