Eelgrass (Zostera marina L.), an underwater marine flowering plant, has a high degree of morphological plasticity that allows it to survive and adapt to environmental changes. To test the effect of eelgrass genetic diversity (measured as allelic richness and observed heterozygosity) on resilience to stresses associated with eutrophication, eelgrass from ten genetically differentiated populations was studied in outdoor mesocosms. In a full factorial experiment lasting 3 months, eelgrass was subjected to two light levels (100 and 58% ambient) and two sediment treatments (1 and 8% organic content). Some populations of eelgrass showed higher resilience, measured as a combination of productivity and survival, when exposed to the stress of high sediment organic matter and, to a lesser extent, reduced light. Overall, eelgrass resilience correlated positively with eelgrass source population genetic diversity. The findings show that eelgrass resilience to stress typical of eutrophic estuaries (low light, high organic sediment) is improved by genetic diversity, with implications for transplantation, conservation, and management.