Understanding the concordance between aquatic assemblages in ecological assessments and their responses to human-induced disturbances are fundamental steps toward achieving sustainable stream and catchment management. Using diatom, macroinvertebrate, and environmental data collected from northwest Chinese arid-land streams, we tested the concordance between the two assemblages in (1) the assessment results using multimetric indices (MMIs), (2) the stressors affecting the MMIs and beta-diversity, and (3) the response trajectories of MMI and beta-diversity to disturbances. Random Forest analyses revealed that diatom and macroinvertebrate metrics responded most sensitively to climatic and geomorphic variables, respectively. Diatom MMI scores had greater precision and responsiveness than macroinvertebrate MMI scores. Diatom MMI scores were negatively related to gradients in observed–expected conductivity, chemical oxygen demand, and vegetated riparian zone width. Macroinvertebrate MMI scores responded strongly to observed–expected mean substrate composition, conductivity, and phosphate. Diatom beta-diversity decreased, as nitrate, channel alternation, and phosphate increased beyond expected natural background levels. Macroinvertebrate beta-diversity was the lowest when both nitrite and % cobble neared their natural background expectations. Our results indicate that protecting aquatic systems from anthropogenic pressures depends not only on revealing causes of impairment, but also on anticipating and understanding the responses to various stressors of multiple stream biotic assemblages.