Previous research concerning the effect of land reclamation on seawater intrusion mostly focused on the modification of the saltwater wedge and the dynamics of freshwater-saltwater interface after land reclamation, utilizing both analytical and numerical models. So far, the impact of land reclamation on the recharging and accumulation of land-based pollutants such as nitrate has been disregarded. In this work, we are the first to examine the impact of land reclamation on the discharge of nitrate together with the movement of saltwater. The influence of reclamation area and filled soil permeability on nitrate pollution and saltwater redistribution is revealed using a series of field-scale simulations based on numerical models including density flow combined with reactive transport. It was discovered that land reclamation might, on the one hand, result in a substantial redistribution based on the initial saltwater-freshwater interface and, on the other hand, significantly modify the nitrate discharge. This in total would drastically alter the distribution of nitrate in the subsurface. The reclamation area and the permeability of the reclamation material are the two elements that determine the amount of variance. For the cases with hydraulic conductivities increasing from 5 to 50 m/d, the salt mass reduction rate showed a trend of first increased (84.78 %–95.58 %) and then slowly decreased (95.58 %–74.01 %). Meanwhile, the nitrate reduction rate decreased from 80.08 % to 12.93 %, when hydraulic conductivities increased from 5 to 50 m/d. It was also found that coastal nitrate accumulation was always intensified with the enlargement of the reclamation area. Finally, we are able to assist engineers in optimizing their land reclamation strategies by taking into account both the degree of saltwater intrusion and nitrate enrichment.