The study objectives were to evaluate the aquatic environment of an urban stream using various ecological parameters of biological biomarkers, physical habitat and chemical water quality and to develop a “Multi-metric Eco-Model” (Mm-E Model) for the ecosystem evaluations. The biomarkers of DNA, based on the comet assay approach of single-cell gel electrophoresis (SCGE), were analyzed using the blood samples of Zacco platypus as a target species. The condition factor (CF) as key indicators of the population evaluation indicator was analyzed along with the weight-length relation and individual abnormality. The four metrics of Qualitative Habitat Evaluation Index (QHEI) were added for the evaluations of physical habitat. In addition, the parameters of chemical water quality were used as eutrophic indicators. Our results suggested that attributes of biomarkers and bioindicators in the impacted zone (Iz) had sensitive response largely to the chemical stress (eutrophic indicators) and also partially to physical habitat quality, compared to the those in the control zone. Hereafter, applying Multimetric Eco-Model to stream ecosystem, it will be able to evaluate ecological health state.