Seagrass beds have decreased in abundance and areal coverage over the past several decades. Although previous studies have examined the importance of seagrass for benthic community assemblages and abundances, the effect of seagrass on deep-dwelling, large (high-biomass) infauna and the importance for benthic secondary production in Chesapeake Bay have not been addressed. Using benthic suctions and push cores, we compared density, diversity, and secondary productivity of benthic communities in seagrass to those in other shallow-water habitats and estimated benthic secondary productivity lost in the York River due to loss of seagrass from 1971 to 2016. We examined four habitat types in the York River: unvegetated, Gracilaria spp., mixed seagrass (multiple seagrass species), and Zostera marina L. seagrass. Physical characteristics of habitat types and biomass of organisms were assessed, and annual secondary productivity was calculated using biomass and production-to-biomass ratios. Benthic density, diversity, secondary productivity, sedimentary chlorophyll a, and percent sand were all highest in seagrass beds with Z. marina alone. Approximately 35% of benthic secondary productivity, or 1.51 × 108 g C yr–1, was lost in the York River in 1971–2016 due to the loss of seagrass beds to unvegetated substrate. The loss of seagrass in the York River over time and the associated decrease in benthic secondary productivity that we estimated could have negative consequences for the productivity of epibenthic predators. Our data emphasize the importance of conservation and restoration of seagrass.