Data concerning the planktonic food web and the farmed pearl oysters of the lagoon of Takapoto Atoll were assembled into a steady state model of carbon flows. A method of optimisation, using constraints from the literature, called ‘inverse analysis’ was chosen as the numerical tool for estimating the missing flow values. The resulting food web is characterised by: 1) high primary production, achieved by low phytoplankton biomass, 2) high production of non-living matter, especially as dissolved organic carbon, 3) low bacterial production, 4) zooplankton dominated by protozoa (biomass and processes) and mesozooplankton (processes), and 5) very low consumption of plankton by farmed bivalves compared to planktonic fluxes. When considering the whole lagoon, the farmed oysters (Pinctada margaritifera) and associated bivalves (Pinctada maculata) consume 0.24% of the planktonic gross primary production. In addition, the consumption by natural populations of the main benthic bivalves in this lagoon (Chama iostoma, Arca ventricosa, Pinctada margaritifera and Pinctada maculata) is also low compared to the high planktonic primary production (4.1%). The oyster farming in this lagoon is thus very far from being food-limited.