Wetlands, especially marshes, support many services such as carbon catchment control or water purification led by primary producers such as phytoplankton and microphytobenthos (PB). The impact of the sedimentary compartment, as source and sink of essential nutrients for the water column, is often neglected in the study of their dynamics and water purification capacity of the systems. This work compared monthly (between February 2020 and April 2021) the benthic and pelagic primary producers’ dynamics in two anthropised freshwater marshes (Marans and Genouillé), with the simultaneous follow-up of physico-chemical parameters of the water column and nutrient fluxes at the sediment-water (SWI) interface. It was suggested a strong contribution of phytoplankton (pumping) and the benthic compartment (denitrification) to the water purification of these two nitrates (NO3-)-rich marshes. Total phytoplankton production fluctuated between ~5 (winter) and 1500 mg C m-3 d-1 (fall) at Marans and between 40 (winter) and ~750 mg C m-3 d-1 (spring) at Genouillé. At Marans, soluble reactive phosphorus (SRP) benthic effluxes (-2.101 to -6.102 µmol m-2 d-1 in fall and summer respectively) coincided with phytoplankton bloom periods. These effluxes were inhibited by NO3- penetration in the sediment (0 to 5.104 µmol m-2 d-1), by inhibiting iron respiration. At Genouillé, inhibition of SRP effluxes depended on denitrification rate and on P stocks in the sediment, where slight SRP effluxes (-101 µmol m-2 d-1) could have co-occurred with slight NO3- influxes (5.102 µmol m-2 d-1) in spring. The presence of PB (between 10-60 and 40-120 mg gsed-1 at Marans and Genouillé respectively), suggested a strong contribution of the benthic compartment to the total primary production (benthic and pelagic through resuspension processes) in these environments. This work encourages to consider the benthos and the pelagos as a unicum to provide better sustainable management of such systems and limit eutrophication risks in coastal areas.