This study investigated the fouling of four polyamide nanofiltration membranes by two surface waters that differed substantially in major properties. The emphasis was on determining the characteristics of the fouling layer on the membranes. The rates of fouling for the two waters differed considerably, with a more rapid flux decline being observed for the water having higher biopolymer and major ion concentrations. Measurements of membrane roughness, contact angle and zeta potential in general showed considerable differences for each of these properties among the virgin membranes. However, values of each of these parameters tended to converge for all membranes after fouling, regardless of which water had been used. This result is very significant (for example for the removal of trace contaminants, which in many cases may depend on membrane properties) because in practice a membrane spends virtually all of its operating life fouled to some degree. Several techniques including transmission electron microscopy (TEM) were used to conduct detailed investigations of the fouling layer. These results demonstrated the great heterogeneity within that layer, despite the similar overall properties mentioned above. This heterogeneity is significant for quantitative understanding of the relationship between fouling and flux and for strategies to reduce or remove fouling.