We sampled stream physical habitat, water temperature, and fish and macroinvertebrate communities at multiple paired watersheds before and after BMP installation from 1993 to 1999 to examine the responses of stream quality to watershed-scale BMP implementation. Our results clearly demonstrated that watershed-scale BMP installation significantly (p < 0.10) improved stream habitat quality, bank stability, instream cover for fish, catch of cool-and coldwater fishes, and catch of all fishes. Stream benthic macroinvertebrate community and water temperature showed consistent trends of improvement relative to the reference sites but were not statistically significant. The first catch of naturally reproduced trout in 1999 indicates Spring Creek has gained the ability to partially sustain its trout population because of overall stream quality improvement. Our results collectively demonstrated that watershed and riparian BMP implementation improve overall stream quality and our approach, studying multiple paired watersheds with before-and after-treatment data, proven effective in detecting the response of stream quality to BMP implementation.