The integrative approach for ecological stream health assessments was applied to a stream ecosystem using a multi-level organization from molecular level of biomarkers to community levels of bioindicators along with analysis of physical and chemical stressors. Water quality parameters of BOD, COD, TN, and TP etc were measured and physical habitat health, based on Qualitative habitat Evaluation Index (QHEI) model were analyzed. Also, Ecological stream health model, based on index of biological integrity (IBI) by fish assemblage, was developed for regional assessments and then applied to the stream. Six metric attributes of original 11 metrics were modified for a development of the model. Biomarkers of comet assay, blood chemistry, physiological parameters, and bioindicators such as organismal-, population-, community- level parameters were evaluated in this study along with eco-toxicity tests. Some stations impaired (stressed) in terms of stream health were identified by the IBI approach and also major key stressors affecting the health were identified using BOD, TN, TP, physical habitat evaluation, and eco-toxicity tests. The assessment approach of integrative ecological stream health would be used as a key tool for ecological restorations and species conservations in the degraded stream ecosystems and applied for elucidating major causes of ecological disturbances. Ultimately, this approach provides us an effective management strategy of stream ecosystems through establishments of ecological networks in various watersheds. This research was supported by Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education (No. 2013R1A1A4A01012939).