A bioenergetics model of the Manila clam (Ruditapes philippinarum) was built to simulate growth, reproduction and spawning in culture and fishery field sites in Marennes–Oléron Bay (French Atlantic coast). The model is driven by two environmental variables: temperature and food supply. Food supply and the clam's filtration rate determine soft tissue condition index, which in turn drives clam growth and reproduction. The model was calibrated and then validated using two independent data sets. This paper discusses the difficulty of comparing experimental data and individual model outputs when asynchronous spawning events occur in the studied population. In spite of this difficulty, the simulations reproduce the typical pattern of growth and reproduction of the Manila clam. Simulations showed that water column chlorophyll a concentration is not a perfect estimator of food resources for a near bottom suspension feeder such as the Manila clam and emphasize the lack of knowledge about Ruditapes philippinarum nutrition. The individual growth model presented in this paper will be integrated into a numerical population model describing the host–parasite–environment relationship in Brown Ring Disease, caused by the bacterium Vibrio tapetis.