Environmental benefits are one of the motivations for management restoration of depleted bivalve populations. We describe a series of linked modules for benefits calculation. The modules include: oyster (Crassostrea virginica) bioenergetics, materials transport via the tidal prism, and benefits quantification. Quantified benefits include carbon, nitrogen, and phosphorus removal and shell production. The modules are demonstrated through application to the Great Wicomico River, a tributary of Chesapeake Bay, USA. Oysters on seven reefs (total area 2.8 × 10(5) m(2)) are calculated to remove 15.2, 6.2, and 0.2 tons per annum of carbon, nitrogen, and phosphorus, respectively, from the Great Wicomico. Oyster mortality contributes 108 tons per annum dry weight shell to the reefs.