Numerous studies have pointed out the importance of groundwater and surface water interaction (SW–GW) in a river system. However; those functions have rarely been considered in large scale hydrological models. The SWAT-LUD model has been developed based on the Soil and Water Assessment Tool (SWAT) model; and it integrates a new type of subbasin; which is called subbasin-LU (SL); to represent the floodplain area. New modules representing SW–GW exchanges and shallow aquifer denitrification are developed in the SWAT-LUD model. In this study; the SWAT-LUD model was applied to the middle floodplain area of the Garonne catchment in France. The results showed that the SWAT-LUD model could represent the SW–GW exchange and shallow aquifer denitrification appropriately. An annual 44.1 × 10 7 m 3 of water flowed into the river from the study area; but the annual exchanged water volume was 6.4 × 10 7 m 3 ; which represented just 1% of the river discharge. A total of 384 tons of N-NO 3 − (0.023 t·ha −1) was consumed by denitrification in the floodplain shallow aquifer annually. The nitrate concentration (N-NO 3 −) decrease in the channel was 0.12 mg·L −1 ; but in the shallow aquifer it reached 11.40 mg·L −1 ; 8.05 mg·L −1 ; and 5.41 mg·L −1 in LU1; LU2; and LU3; respectively. Our study reveals that; in the Garonne floodplain; denitrification plays a significant role in the attenuation of nitrate associated with groundwater; but the impacts of denitrification on nitrate associated with river water is much less significant.