Desalination is important in artificial groundwater recharge with reclaimed water for minimizing the effect of salinity on groundwater and soil quality. In this study four kinds of nanofiltration membrane, as the compensatory process in soil treatment, are embedded into enhanced direct injection-well recharge (EnDir) for desalination purposes. The lab-scale experiments indicate that nanofiltration (NF) in the sequence of short-term soil treatment provides additional removal of organic and inorganic compounds. NF90 exhibits a marked superiority over the other types of membrane, with respect to the desalinization of reclaimed water. The removal efficiencies for total dissolved solids (TDS) and alkalinity amount to 89% and 96%, respectively. For the anions in the reclaimed water, NF90 exhibits 80% removal efficiency for nitrate, 94% for chloride and 99% for sulphate, which are removed to a limited extent in the soil treatment. The sodium adsorption ratio (SAR) value of NF90 permeate is the lowest among these membranes, which minimizes the risk of sodification associated with soil structure degradation during artificial groundwater recharge. In addition, NF90 can reduce the concentrations of heavy metals in the reclaimed water to far below the national standards for groundwater.