The objectives of this study were to evaluate how chemical gradients and physical habitats influence trophic dynamics and chemical tolerance in relation to ecological health, based on biological integrity model in the absence of cascading pressures (cascading theory) as a control mechanism of aquatic ecosystems. We conducted physical, chemical, and biological surveys from 76 national streams and rivers of four major watersheds during 2004Á2005 along with surveys of 80 reference streams. Maximum species richness lines (MSRLs) in reference sites vs. regular sampling sites indicated that the third-to fifth-order streams were evidently impaired in the metrics of trophic and tolerant components. These trophic modifications were linked with land-use patterns, which resulted in differences of nutrients (N, P), organic matter contents and the N:P ratios on trophic structures. Overall, these trophic factors influenced ecological health, based on multimetric index of biological integrity model in these systems, so that trophic compositions and tolerance were regulated by bottom-up hypothesis.