Environmental factors and epilithic diatom communities in the lower streams near the harbor region of South Korean peninsula were examined during no monsoon period in May 2013. The sampling of water and epilithic diatoms was conducted at both streams, 19 regulated streams (RS) that there are one or several dams constructed in the river system, and 19 un-regulated streams (US) that there are no dams within the river. A cluster analysis based on the number of species and abundance of epilithic diatoms through the stations, divided into three groups such as groups I (mainly US), II (mixed with US and RS) and III (mainly RS), respectively. Group I showed that water quality is good and high diversity of diatom, while Group II and III was water quality is relatively poor, but not differed in biomass of diatom from Group I. In addition, Group II that had high conductivity, nitrogen and phosphorus, was the lowest in diatom diversity among them. Dominant species were Nitzschia palea (17%) and Navicula seminuloides (11%) in Group I, Nitzschia inconspicua (19%) and Navicula perminuta (9%) in Group II, and Nitzschia inconspicua (15%) and Nitzschia palea (14%) in Group III, respectively. These taxa were widely distributed in brackish water, and not closely related with specific water quality, like eutrophic water. However, the groups II and III belonged to RS, had not only little biomass, but bad water quality such as high concentrations of nutrient and chlorophyll-a. Therefore, to determine the effect of dam construction on the lower water ecosystem, the planktonic algae, which can occur algal bloom in the estuary, also was considered to be a parallel investigation.