Recent research has demonstrated the important role that high-biomass species play in the transfer of energy and nutrients across habitat boundaries, as well as the ecosystem consequences of their loss. To contrast the historical and current biomass of historically abundant anadromous forage fish, we combined historical records of habitat loss from damming with contemporary freshwater productivity of alewives and diet data of freshwater predator fish. Significant declines in production occurred by 1850 in the northeastern United States, long before any direct abundance data were available, which would have had significant effects on freshwater prey resources for the numerous predators directly affected by the transfer of nutrients across the freshwater–marine nexus. Current freshwater systems operate at approximately 6.7% of historical capacity of anadromous alewife biomass and abundance. This provides an example of habitat-mediated changes in connectivity limiting nutrient flux and energy flow among populations and species that alter ecosystem function at multiple scales.