The Mediterranean Sea (MS) is a large oligotrophic sea whose productivity is sensitive to riverine nutrient inputs. More specifically, phosphorus (P) river supply is crucial for the MS, with an important role of the estuarine/deltaic filter especially for the storage and recycling in sediments. A benthic dataset from the Rhône River prodelta was used to derive P budgets, by means of an early diagenetic model including the benthic P cycle. The model was fitted to pore water profiles of oxygen, nitrate, sulfate, dissolved inorganic carbon, ammonium, oxygen demand units, dissolved inorganic phosphorus (DIP) and solid data (organic carbon (OC), Fe-bound P, Ca-bound P and organic P). Results indicated that the intensity of biogeochemical processes occurring below the sediment–water interface decreased from the river mouth to the adjacent continental shelf with decreasing integrated rates of OC mineralization (160–10 mmol m−2 day−1). The organic P mineralization was intense near the river mouth and decreased offshore (1196–80 μmol m−2 day−1). Its contribution to DIP release was large (> 90%). Fe-bound P had a key role in transferring P to deeper layers. These deltaic sediments played an important role as a source of regenerated DIP. A significant part of DIP was recycled to the overlying waters (72–94%), representing 25% of the riverine DIP discharge. Simultaneously, 6–28% of DIP produced in sediments was buried as Ca-bound P. Overall, this study highlighted the importance of deltaic sediments as an additional source of DIP to the coastal sea, and a minor but permanent sink of phosphorus as solid P burial.