The nanofiltration of dairy ultrafiltration permeate can be used to produce a concentrated lactose product that is reduced in unwanted monovalent salts. In this paper, the surface charge of three nanofiltration membranes commonly used for such a purpose is examined. The focus is the impact of multivalent anions, notably phosphate and citrate, upon the surface charge of the membranes within a ternary system of potassium and calcium chloride. It was shown that these multivalent anions can influence the membrane charge through interactions with calcium, even though they are unlikely to adsorb to the membrane surface. Specifically, both phosphate and citrate can form soluble charged species with the calcium ions, reducing the net Ca2+ concentration and hence the overall effect of calcium on the membrane. This ion interaction effect becomes more dominant at higher pH values, due to the greater tendency of calcium to interact with either phosphate or citrate at higher pH.