BACKGROUND: In the removal of pharmaceuticals present in aquatic systems by membrane processes, some important issues must be explored in order to obtain a better knowledge of the global process. Among these issues, a better understanding of the influences of the operating parameters on the membrane flux, an analysis of membrane resistances and fouling, and determination of the removal of specific substances, must be studied. RESULTS: Four selected pharmaceuticals (amoxicillin, naproxen, metoprolol and phenacetin) were subjected to ultrafiltration (UF) and nanofiltration (NF) processes for their removal from several water matrices. The determined permeate fluxes at the steady state were affected by the main operating conditions: molecular weight cut-off (MWCO) of the membrane, transmembrane pressure TMP, cross-flow velocity and temperature. The retention coefficients with the UF membranes followed the sequence naproxen > metoprolol > amoxicillin > phenacetin, and with the NF membranes, followed the trend: amoxicillin > naproxen > metoprolol > phenacetin, due to the role of other mechanisms such as size exclusion and electrostatic repulsion. In the case of the selected water matrices, the retention coefficient was referred to some quality parameters (total organic carbon, chemical oxygen demand and absorbance at 254 nm), leading to moderate (UF) or high (NF) removals of the organic matter content. CONCLUSIONS: The NF CK membrane achieved the highest retention of these pharmaceuticals (excepting phenacetin), and provided retentions for quality parameters around 80% in the four water systems tested. (C) 2011 Society of Chemical Industry