The influence of membrane fouling on the retention of pharmaceutically active compounds (PhACs) by three nanofiltration membranes was investigated in this study. Membrane fouling was achieved with a foulant cocktail containing model organic foulant in a background electrolyte solution. The effects of membrane fouling on the separation process was delineated by comparing the retention values of clean and fouled membranes and relate them to the membrane properties as well as physicochemical characteristics of the PhACs. Fouling was more severe for the larger pore size TFC-SR2 and NF 270 membranes as compared to the smaller pore size NF 90 membrane. More importantly, the influence of membrane fouling on the retention of PhACs was found largely dependent upon membrane pore size. It was hypothesised that such influence was governed by three distinctive mechanisms: modification of the membrane charge surface, pore restriction, and cake enhanced concentration polarisation. The presence of the fouling layer could affect the retention behavior of charged solutes by altering the membrane surface charge density. While the role of this surface charge modification mechanism was clear for inorganic salts, it was less obvious for the negatively charged pharmaceutical species examined in this investigation, possibly due to the interference of the pore restriction mechanism. Behavior of the very loose TFC-SR2 membrane was found dominated by pore restriction and this membrane consistently showed an increase in retention under fouled conditions. In contrast, evidence of the cake enhanced concentration polarisation effect was observed with the smaller pore size NF 270 and NF 90 membranes. Crown Copyright (c) 2007 Published by Elsevier B.V. All rights reserved.