Using large-scale field surveys across 12 estuaries in two provinces in Atlantic Canada, we analyzed changes in phytoplankton and benthic macroalgal communities as well as the canopy structure of eelgrass beds and quantified their carbon and nitrogen storage with increasing eutrophication. As eutrophication increased, phytoplankton biomass increased on average 1.8 times and phaeopigments doubled. Among macroalgae, the epiphytic Ulothrix speciosa increased 40 times in New Brunswick, and benthic Ulva lactuca 670 times in Prince Edward Island covering 61% of the bottom. Eelgrass showed a significant increase in leaf length and declines in shoot density and aboveground and belowground biomass, consistent with increased shading by opportunistic algae. As eelgrass biomass declined, so did the carbon storage capacity of the habitat. Nitrogen storage only declined in belowground eelgrass beds due to increasing tissue nitrogen content above ground with eutrophication. Despite province-and species-specific responses of primary producers to nutrient loading, principal component analysis revealed an overall shift from perennial eelgrass to opportunistic macroalgae and phytoplankton with eutrophication at the regional scale, indicating generalized eutrophication effects on primary producer assemblages.