Different biological groups show biased responses to similar or different environmental stressors on different scales. The selection of bioindicators based on pressure characteristics is the basis for accurately assessing ecological quality. In this study, we investigated the responses of common bioindicators, namely, macroinvertebrates and fish, to multiple stressors in temperate mountain and plain streams of northeast China. We used 56 indices, including the single biological evaluation index and biological evaluation index system, to analyze and compare characteristic response to different scales under varying environmental stressors. The principal component analysis (PCA) showed that PCA axis 1 in the catchment scale explained 83.6% and 96.1% of the variance in mountain and plain rivers, respectively, which characterized the comprehensive pressure gradient integrated by land-use development and water pollution. PCA axis 1 explained 40.7% and 53.9% of variance in mountain and plain rivers on the reach scale and 63.1% and 61.8% of variance on the site scale. The correlation analysis showed responses of different indices to abiotic variables which did not overlap. Macroinvertebrate and fish indices successfully explained the change in water chemistry on a small scale, whereas fish indices additionally explained the change in land use on a large scale. Macroinvertebrate and fish indices were recommended because of their rich responses to environmental stressors, particularly in plain rivers. For mountain stream biomonitoring programs, especially in the Taizi River of northeastern China, we suggest that macroinvertebrates and fish should be used separately or jointly according to the actual capacity and cost, Moreover, compared with the possible differences in the evaluation results of different single biological evaluation indexes, the biological evaluation index system shows more stable monitoring results, and the single sensitivity index is more significant in biological evaluation, and more sensitive to some special environmental factors. © 2021 by the authors. Licensee MDPI, Basel, Switzerland.