The aim of this work was to provide a first estimation of the overall contribution of pearl oyster culture to nutrient regeneration in a deep atoll lagoon. Nutrient release by pearl oyster culture in the water column and nutrient fluxes at the sedimentewater interface were compared in two contrasted conditions (i.e. under the influence or not of pearl oyster farming) in the Ahe atoll (French Polynesia). Nitrogen flux intensity was higher in the water column than at the benthic interface. Nitrogen was released at a rate of 31.36 mmol h À1 m À2 in the water column and 12.05 mmol h À1 m À2 at the sedimentewater interface. Average phosphorus flux was 2.85 mmol h À1 m À2 at the sedimentewater interface and 2.16 mmol h À1 m À2 in the water column. In this deep lagoon, pearl oyster culture exerted more influence in the pelagic compartment than at the benthic interface where flux rate seemed not to be influenced by the presence of pearl oyster culture. These results demonstrate that it is essential to study these two interfaces in concert when assessing the impact of suspended shellfish farming on nutrient dynamics. Overall, the impact of pearl oyster culture may stimulate phytoplankton growth near cultivation areas through the rapid recycling of inorganic nutrients.