Ecological risk assessment was carried out in two urban streams, viz. Gap Stream (GS) and Miho Stream (MS), in the Geum River Watershed during July 2013-October 2014. The techniques used in this study included multi-level fish biomarkers of DNA damage based on single-cell gel electrophoresis (SCGE) coupled with the study of physiological responses based on 7-ethoxyresorufin-O-deethylase (EROD) and acetylcholinesterase (AChE) activities in fish species. Biomarker values of tail DNA (tDNA), tail length (T_L), and tail extent moment (TEM) in impacted zone (I_z) were 2.0-3.6-fold greater than in controls (C_z). Nucleus image analysis showed that the nucleus had circular particle forms in the C_z as compared with a longitudinal oval form with broken particles from the nucleus in the I_z. Physiological response analysis of EROD and AchE activities indicated that their levels were higher in the I_z than in the C_z. Such DNA damages and greater physiological responses in the I_z were attributed to chemical contaminants discharged from the wastewater disposal plants and industrial complex. This combination of DNA damage and physiological responses approach can be used as a key tool for early-warning detection of chemical contaminants and concomitant risks to the ecological health of urban streams.