A coupled hydrodynamic-biogeochemical modelling is developed to address main mechanisms that drive the particulate organic carbon (POC) deposition in the Gulf of Lions (NW-Mediterranean). Low-salinity water (LSW, salinity < 37.5) lenses detached from the Rhone River plume under specific wind conditions tend to favour the biological productivity and provide a good opportunity for validating a planktonic ecosystem modelling. A specific calibration dedicated to river plume ecosystems is then proposed and validated using in situ measurements within such LSW lens (BIOPRHOFI cruise - May 2006) and on the Gulf of Lions. During spring 2006, the POC deposition is maximal on the prodelta area and within the coastal area in the Gulf of Lions. Organic detritus mostly contribute to the total POC deposition (82-92 %) whereas the contribution of living organisms (microphytoplankton) appears lower than 17 %. Exploring both influences of terrestrial inputs from the Rhone River and planktonic ecosystems on the POC deposition on the shelf, we estimated that the contribution of terrestrial POM inputs to the total POC deposition is lower than 17% at the shelf scale during the study period, with maxima during peak discharges of the Rhone River. The main deposition area of terrestrial POC is found in the vicinity of the river mouth in agreement with sediment data. On the other hand, a remarkable influence of marine biological processes on the POC deposition is highlighted further on the shelf (from 60 to 80m depth). A tight feedback between zooplankton and POM contents in the water column is proposed to explain the control of POC deposition by zooplankton: terrestrial POM inputs would favour the development of living organisms through photosynthesis and grazing processes increasing the retention of organic matter within the food web. By favouring the development of large-sized zooplankton, LSW lenses may have paradoxically a negative impact on the carbon deposition on the shelf. In the same way, peak discharges of the Rhone River finally increase the gradient of POC deposition between the prodelta and the offshore area in the Gulf of Lions. The biogenic elements from the Rhone River are then exported further offshore through advection of zooplankton communities on the Gulf of Lions shelf.