Epilithic diatom communities and water quality were monitored to evaluate the ecological impact of the inflow of Wonju-stream passing through the urban area in the Seom River Watershed. We selected the 14 sampling stations (5 main stream sites and 9 tributary sites), and collected diatom and water samples between October 2007 and September 2008, on the seasonal basis. The results indicate that most water quality parameters showed the site-specific patterns over the study, except for water temperature and dissolved oxygen. The levels of water quality parameters were highest at the site of Wonju stream, whereas the lowest in the upstream sites, and intermediate or gradually decreased in the downstream sites of the Seom river. One species, Achnanthes convergens, showed the highest biomass and frequency over the sites, while three saprophilous species-Navicula goeppertiana, Navicula subminuscula, Nitzschia palea were appeared only in Wonju Stream and other polluted sites. According to trophic diatom index (TDI) values, which were highly correlated with nutrients and EC, the study sites were classified into three classes: upstream and tributary (Class A and B), Wonju Stream (Class D), and mixed zone and downstream (Class C). A cluster analysis supported the result of TDI classification. Therefore, Wonju-stream located in populated urban area exerted the adverse ecological effects on the epilithic diatom community and water quality of the lower Seom River System, although its severity gradually decreased downstream.