This study investigated the efficiency of mycoestrogens removal from water using the sequential combinations of two processes: ozonation and nanofiltration. The results were compared with ones obtained for water treatment via ozonation and nanofiltration performed as single-stage operations. The removal of mycoestrogens was improved using the combination of ozonation–nanofiltration processes in comparison to single-stage ozonation system, while a negligible difference was observed with nanofiltration. However, the analyzed system improved the nanofiltration membrane capacity. Ozonation before membrane filtration limited the intensity of the membrane blocking, which adjusted the use of the complex systems in water treatment.