Little is known about DNA-level and physiological levels for health assessments of stream or river environments. Recently, comet assay, so called Single Cell Gel Electrophoresis (SCGE) is introduced for assessments of DNA damage in the medical science, food science and mammal toxicology. The comet assay is known as a biomarker which is one of the best barometers in assessing the DNA damage by oxidative stress. In this study, we conducted the comet assay using sentinel species, Zacco platypus, as one of the pre-warning alarm systems for the aquatic ecosystem health assessments and also applied it to Gap Stream as a model system. Tail extent moments in the S1 and S2 were 5.20 and 9.90 respectively and the moment was 19.89 in the S3. Statistical ANOVA in the tail moments showed a significant difference (n=75, p<0.05) between S1 and S3. Also, the proportions of DNA in the tail were 14.47, 23.64, and $30.04{mu}m$ in the upstream (control site), midstream, downstream sites, respectively. Our results in the downstream were accord with previous studies of individual-level, population-level, and community-level in Gap Stream. Our results suggest that the comet assay may be used as an important tool for diagnosing ecological health of aquatic ecosystems in the level of DNA.