Abstract Most nanofiltration membranes are composite and have a polyamide thin film prepared by interfacial polymerization. Their characteristics and performance are mainly determined by the thin film and consequently by the monomers used for its preparation. In this work, different thin films were prepared with small structural differences to help understanding how the amines structure influences the membranes nanofiltration performance, surface charge and morphology. Composite membranes were prepared by interfacial polymerization of piperazine (PIP), N,N ′-diaminopiperazine (DAP), 1,4-bis(3-aminopropyl)-piperazine (DAPP) and N -(2-aminoethyl)-piperazine (EAP) with trimesoylchloride (TMC) separately. Their nanofiltration performance was evaluated with solutions of NaCl, MgSO 4 and Na 2 SO 4 (3 g/l and pH 6) at 10 × 10 5 Pa. The surface charge was investigated by zeta-potential measurements and the morphological studies by atomic force microscopy (AFM) and scanning electron microscopy (SEM). The average water permeability of the samples was correlated with hydrophobic/hydrophilic character of the monomers by use of the octanol–water partition coefficient. At pH 6 the membranes from PIP, DAP and EAP presented the following order of rejection NaCl 4 2 SO 4 characteristic of negatively charged membranes. The rejection order of the DAPP–TMC membrane was Na 2 SO 4 4 since it was positively charged at pH 6. The membranes surfaces were in general flat except for the PIP–TMC membrane which had higher roughness. The DAP– and EAP–TMC presented an extremely thin film, undetectable by SEM analysis of the membranes cross-section.