Stream restoration projects are increasingly common. However, restoration projects that establish measurable goals, have pre- and post-restoration monitoring, and are implemented at the watershed scale are rare. We conducted a long-term (9-year) before-after-control-impact designed assessment of two watershed-scale acid mine drainage (AMD) remediation programs, one in a warm-water ecosystem and one in a cold-water ecosystem in West Virginia, USA. Restoration was strategically designed to recover biodiversity and improve the native fisheries by restoring chemically degraded water quality and re-establishing riverscape connectivity. We used analysis of variance to quantify responses in water chemistry, benthic macroinvertebrate communities, and fish community composition before and after restoration within and among treated and un-treated sites. Assessments within the warm- and cold-water watersheds show significant improvements post-restoration in water quality and macroinvertebrate communities in both watersheds. However, differences in fish community responses indicate that regionally degraded conditions may play a role in the ability of fish communities to recover in restored systems. Fish diversity increased to reference conditions in both watersheds but functional fisheries are not recovering. In the warm-water system, the reference sites do not meet the regional drainage area to species richness relationship whereas the cold-water system has intact reference populations within the watershed. This suggests that successful fishery restoration in degraded watersheds depends on the presence of a regional species pool available to repopulate the targeted watershed. Furthermore, long-term changes in fish communities in the cold-water system indicate that fish populations may have a delayed response to restoration projects. Treated sites within the cold-water watershed had significant improvements in water chemistry and macroinvertebrates from 2008 (i.e., pre-restoration) to 2013 and remained unchanged from 2013 to 2017. However, fish diversity and brook trout populations in treated streams increased significantly from 2008 to 2013 and continued to increase in 2017. The continued increase in brook trout populations over time suggests that restoration was successful in reestablishing connectivity among restored and previously intact brook trout sub-populations. Consequently, the full benefit of restoration may not yet be realized as fish populations continue to expand