Artificial reefs (ARs) are widely used for fisheries management. Research has shown that a mechanism by which ARs in seagrass beds can support fisheries and carbon sequestration is through increasing primary production via fertilization from aggregating fish excretion. Seagrass beds are heavily affected by anthropogenic nutrient input and fishing that reduces nutrient input by fish. We used a long-term experiment to identify the mechanisms by which simultaneous impacts of sewage enrichment and fishing alter seagrass production around ARs across non-orthogonal gradients in human-dominated and relatively unimpacted regions in Haiti and The Bahamas. Merging trait-based measures of seagrass and seagrass ecosystem processes, we found that ARs consistently enhanced per capita seagrass production and maintained ecosystem-scale production despite drastic shifts in controls on production from human stressors. These findings emphasize the resilience of seagrass ecosystems and the positive impact ARs can have on ecosystem services in human-dominated areas. Our research provides valuable information for the conservation and management of seagrass ecosystems and the role of ARs in supporting vital ecosystem services.