Assessing benthic invertebrate community responses to multiple stressors is necessary to improve the success of restoration and biomonitoring projects. Results of mesocosm and field experiments were integrated to predict how benthic macroinvertebrate communities would recover following the removal of acid mine drainage from the North Fork of Clear Creek (NFCC), a U.S. EPA Superfund site in Colorado, USA. We transferred reference and metal-contaminated sediment to an upstream reference site where colonization by benthic macroinvertebrates was measured over 30 days. Additionally, a mesocosm experiment was performed to test the hypothesis that patches of metal-contaminated substrate impede recolonization downstream. Abundance in all treatments increased over time during field experiments; however, colonization was slower in treatments with metal-contaminated fine sediment. Community assemblages in treatments with metal-contaminated fine substrate were significantly different from other treatments. Patterns in the mesocosm study were consistent with results of the field experiment and showed greater separation in community structure between streams with metal-contaminated sediments and reference-coarse habitats; however, biological traits also helped explain downstream colonization. This study suggests that after water quality improvements at NFCC, fine-sediment deposition will likely reduce recovery potential for some taxa; however highly mobile taxa that avoid patches of contaminated habitats can recover quickly.