The carrying capacity of a 2.4 ha Manila clam Venerupis philippinarum farm, using mechanised harvesting in North Puget Sound, WA, USA, was determined by means of an ecological model; the results were also scaled to Puget Sound as a whole. An individual Manila clam growth model was developed, calibrated and validated for the commercial farm, together with a macroalgal model to simulate fouling of the predator nets by seaweeds. Both models are based on our previously developed generic frameworks for bivalves (AquaShell) and seaweeds (AquaFrond). For the most part, equations are taken or adapted from the literature and parameterised for the studied site. The individual models were incorporated into the Farm Aquaculture Resource Management (FARM) model to simulate the production cycle, environmental effects and economic optimisation of culture. Both the individual and farm-scale models are built using object-oriented programming. Potential effects of clam production on seaweed growth were analysed and found to be about 10% above background. The FARM model was also used to classify the farm area with respect to its eutrophication status, by applying the Assessment of Estuarine Trophic Status (ASSETS) model. Farm production ranging from 32 to 45 t of clams per year is well reproduced by the model. Harvest yield is very sensitive to mortality, and profitability is very sensitive to seed costs. Manila clam culture provides a potential nutrient credit trading value of over US $41 000 per year, over 1000 Population-Equivalents (PEQ, i.e. loading from humans or equivalent loading from agriculture or industry) with respect to eutrophication control. The potential income would add 21% to the annual profit ($194 900) from clam sales. A scaling exercise to the whole of Puget Sound is in reasonable agreement with declared production (difference of 16%), and suggests that clams provide a significant ecosystem service, of the order of 90 000 PEQ per year.