The recent development of new mineral and organomineral membranes induced an increasing interest in the nanofiltration process. Their better mechanical as well as chemical properties allow them to challenge widely commercialised organic membranes. In this work, the behaviour of both copper and silver in the course of nanofiltration is studied in presence of nitriloacetic acid (NTA) and sodium thiosulphate. Filtrations were performed using two different types of membrane: a mineral gamma alumina membrane with a point of zero charge equal to 8.2, and an organic membrane (MT34). Effects of the nature of ligand, pressure, pH and metal concentration were examined on each studied membrane. Filtrations on organic membrane showed that only the molecular weight can be considered as an preponderant parameter in relation with the rejection yield. On the other hand, based on both electric interaction and molecule size, the mineral amphoteric membrane allowed various possibilities of separation between the two metals according to the pH value.