This study describes the rejection of heavy metal ions (Cu(II), Cd(II), and Zn(II)) using two commercial nanofiltration membranes (DL and DK). The effect of transmembrane pressure and metal concentration on the metal rejections and permeate flux was explored. The results showed that for DL membrane the maximum rejection was obtained at ΔP = 4 bar for all studied heavy metals. The rejections of Zn, Cu, and Cd were 93, 90, and 86%, respectively, when the concentration of each heavy metal was fixed to 10−5 mol/L and were 79, 76, and 78%, respectively, when the concentration of each heavy metal was fixed to 10−3 mol/L. The rejection sequence was identical for both membranes (RCu < RZn < RCd). However, the transmembrane pressure and the metal concentration had no great effect on rejection factors in the case of DK membrane. The variation of the permeate flux vs. the transmembrane pressure after treating different mixtures containing Cu(II), Cd(II), and Zn(II) metals by nanofiltration using DL and DK membranes was studied. A deviation from the straight line representing Jv vs. ΔP of different mixtures studied compared to pure water line was observed, but it was much more important in the case of DL membrane confirming a greater sensitivity to pores clogging.