This study illustrates changes in the epilithic diatom assemblages in response to urban climatic conditions. We further assess the impact of abnormal urban climate to the urban stream environment. Epilithic diatoms, water chemical and physical variables were sampled every quarter, and assessed at 3 Oncheon stream sites, for a period of two years (from 2013~2014). The variation of physiochemical properties such as BOD, COD, T-N and T-P, show that the water quality was strongly influenced with long periods of drought and flood disturbance. Epilithic diatom assemblages were separated along the stream sites; however, the physical disturbance from urban drought and stormwater changed the composition of diatom assemblages instead of decreasing the taxonomic richness. Thus, our results suggest that epilithic diatom assemblages are altered in response to urban climatic changes, resulting in variations of stream conditions. Hence, strategies of climate change adaptation are required when considering urban stream environments.