Centuries of resource extraction have impacted coral reef ecosystems worldwide. In response, area and fishery closures are often enacted to restore previously exploited populations and reestablish diminished ecosystem function. During the 19th and 20th centuries, monk seals, pearl oysters, and two lobster species were overharvested in the Northwestern Hawaiian Islands, now managed as the Papahānaumokuākea Marine National Monument, one of the largest conservation areas in the world. Despite years of protection, these taxa have failed to recover. Here, we review each case, discussing possible factors that limit population growth, including: Allee effects, interspecific interactions, and time lags. Additionally, large-scale climate changes may have altered the overall productivity of the system. We conclude that overfishing of coral reef fauna may have broad and lasting results; once lost, valuable resources and services do not quickly rebound to pre-exploitation levels. In such instances, management options may be limited to difficult choices: waiting hundreds of years for recovery, actively restoring populations, or accepting the new, often less desirable, alternate state.