The membrane process, i.e. nanofiltration, was considered a method for removal of mycoestrogens, compounds recently identified in aqueous environment, from water. The study was focused on the determination of the separation mechanism and on the possibility of removal of mycoestrogens in the applied process. Retention of zearalenone and α-zearalenol was investigated depending on the water matrix composition, the membrane applied, filtration mode and operating conditions of the process. As removed mycoestrogens reveal hydrophobic character, the separation mechanisms is based on the adsorption. Retention of those compounds is also dependent on the membrane type and the filtration mode. The highest effectiveness of mycoestrogens removal was obtained for cellulose membrane (CK), which characterized the highest values of the contact angle and the degree of NaCl removal in comparison with other composite membranes applied. Additionally, the CK membrane showed the highest ability to adsorb investigated micropollutants. However, the variation of retention of mycoestrogens was observed as the membrane surface was modified by inorganic and/or organic substances present in filtrated water. The degree of removal of mycoestrogens during nanofiltration exceeded 81% and considering the effectiveness and the capacity of the process, the cross-flow mode should be applied.