Separation mechanisms for the three model divalent cations with very similar atomic weights (Cu, 63.5 Da; Co, 58.9 Da and Ni, 58.7 Da) by two nanofiltration (NF) membranes (Nitto Denko ESNA and GE Osmonics DK) were studied in a cross flow module from pHs 3 to 5. The results show that the rejection order for the two selected membranes was Ni2 + > Cu2 + > Co2 + from the conducted experiments, and the removal efficiency was increased as pH was decreased for all three metals. It was found that enthalpy of hydration and concentration polarization exerted the controlling effect on the membrane selective transport rather than atomic weight, Stokes radius and hydrated radius. Besides, the counterion of sulfate enhanced the removal efficiencies, but an increase of sulfate more than 0.01 M reduced the removal efficiencies. Moreover, the removal efficiency of DK membrane was better than that of the ESNA membrane due to the positive charge of DK membrane at low pH.