Marine protected areas (MPAs) have been recommended as an essential conservation tool for ecosystems and fisheries, with MPA coverage increasing four-fold globally since 2000. Despite the increased usage of MPAs, empirical results and scientists are divided on the effectiveness of MPAs to reach their conservation and management goals. In 2009, the South Atlantic Fishery Management Council established eight deep-water partially-protected MPAs off the southeast United States (SEUS) Atlantic coast with the goal of protecting long-lived, deep-water, reef-associated fishery species. Data collected during fish trapping from 2000 to 2018 as part of a fisheries-independent survey were used to evaluate the impacts of protection on a subset of fish species in three of these MPAs. There was a modest positive shift to larger fish observed in two of the MPAs and to older fish for one species, Pagrus pagrus (Linnaeus, 1758), in one of the MPAs relative to adjacent fished areas; however, there was either no change or a decrease in managed reef fish abundance in each MPA relative to adjacent fished areas. Based on these metrics, it does not appear that the SEUS MPAs have yet been effective at protecting managed reef fish species. Given that these MPAs have low enforcement, future assessments should examine compliance within the SEUS MPAs to determine if lack of success is due to illegal fishing, species examined, or MPA design before making a final determination if deep-water MPAs are an effective strategy for fisheries managers in the SEUS.