The object of this study was to evaluate lotic ecosystem health using multiple eco-metric approaches such as water chemistry diagnosis, physical habitat health evaluations, and biological integrity modeling at 100 streams of four major watersheds. For the study, eight chemical water quality parameters such as nutrients (N, P) and organic material were measured and 11-metric models of Qualitative Habitat Evaluation Index (QHEI) and multiple eco-metric health assessment model (MEHA) were applied to the four major watershed. Nutrient analysis of nitrogen (N) and phosphorus (P) in all watersheds indicated a eutrophic state depending on the locations of sampling streams. Physical habitat health, based on the QHEI model, averaged 114 (range: 56 - 194), judging as a "good condition" by the criteria of Plafkin et al. (1989). In addition, primary (H1 - H4), secondary (H5 - H7), and tertiary habitat metric variables (H8 - H11) were analyzed in relation to the physical habitat degradations. The plots of tolerant species ($P_{TS}$) and sensitive species ($P_{SS}$) to water quality showed that the proportions of $P_{TS}$ had positive linear functions with nutrients, and that the $P_{SS}$ had inverse linear relations with the chemical variables. The model of eco-metric health assessment showed that mean MEHA was 20.4, indicating a fair condition. Overall, our data suggest that water chemistry, based on nutrients and organic matter, directly modified the trophic structures in relation to food chain in the aquatic ecosystems, and then these directly influenced the compositions of tolerance/sensitive species, resulting in degradations of overall ecological health.