In coral reef lagoons, microphytobenthos (MPB) primary production can be of the same order of magnitude as coral or macroalgal production. As they are situated in oligotrophic waters, sediments receive low amount of allochtonous nutrients, and their high metabolism cannot be achieved without an efficient nutrient recycling. In oligotrophic environments nutrient exchange between sediments and the water column is considered to be low. However, physical forcing that disturbs the sediment interface may accelerate nutrient exchange. The objectives of this work were to: (i) characterize the benthic trophic status and associated nutrient diffusion fluxes as a function of terrestrial and anthropogenic influence and (ii) investigate the impact of physical forcing on the exchanges at the interface and the response of the water column. For that purpose, a multidisciplinary study was performed in the southwest lagoon of New Caledonia combining field survey, laboratory experiments and mathematical modelling. The field survey indicated that most of the lagoon sediments were autotrophic and presented negligible nutrient fluxes. This suggests an apparent decoupling between the sediment and the water column as long as diffusion is the dominant nutrient exchange mode process. This was confirmed by experimental ex situ incubations that showed bacterial production in the water column was not affected by the presence of sediment. The modelling approach showed that physical forcing, such as sediment erosion or wave driven pore water advection, might enhance the coupling between the sediment and the water column through the release of nutrients and organic matter leading to the stimulation of the bacterioplankton and phytoplankton compartments.