Many coastal habitat restoration projects are focused on restoring the population of a single foundation species to recover an entire ecological community. Estimates of the ecosystem services provided by the restoration project are used to justify, prioritize, and evaluate such projects. However, estimates of ecosystem services provided by a single species may vastly under-represent true provisioning, as we demonstrate here with an example of oyster reefs, often restored to improve estuarine water quality. In the brackish Chesapeake Bay, the hooked mussel Ischadium recurvum can have greater abundance and biomass than the focal restoration species, the eastern oyster Crassostrea virginica. We measured the temperature-dependent phytoplankton clearance rates of both bivalves and their filtration efficiency on three size classes of phytoplankton to parameterize an annual model of oyster reef filtration, with and without hooked mussels, for monitored oyster reefs and restoration scenarios in the eastern Chesapeake Bay. The inclusion of filtration by hooked mussels increased the filtration capacity of the habitat greater than 2-fold. Hooked mussels were also twice as effective as oysters at filtering picoplankton (1.5–3 µm), indicating that they fill a distinct ecological niche by controlling phytoplankton in this size class, which makes up a significant proportion of the phytoplankton load in summer. When mussel and oyster filtration are accounted for in this, albeit simplistic, model, restoration of oyster reefs in a tributary scale restoration is predicted to control 100% of phytoplankton during the summer months.