The effect of membranes' structure on the efficiency of chromium(III) ions recovery from salt solution at low pH and the efficiency of chemical cleaning of these membranes were analyzed in this work. The nanofiltration membranes (DL and HL) used in this study were provided by GE Osmonics. The DL membrane had an irregular, dense support layer structure, while the HL membrane had a loose one. In the case of the DL membrane, it was found that, under tested solutions, the layer of mineral scale formed on the surface gradually decreases the membrane permeability coefficient. In the case of the DL membrane, the scaling was observed only on the surface. On the other hand, a small roughness (118Å) and low density charge (zeta potential at level −4) of the HL membrane causes an uneven growth in deposits and, consequently, irregular nature of the surface structure which hinders the removal of accumulated sediment from the tested membranes' surface. Additionally, the loose structure of the support layer of HL membrane contributes to its internal scaling. Consequently, the permanently loose structure of the HL membrane permeability coefficient was observed.