In continuous ethanol fermentation processes, which include product removal and recovery steps, to limit the concentration of secondary products, a bleed stream may be used. This stream contains several small molecular weight organic fermentation products and substrate sugars. To recover sugars and to minimize the amount of waste, the bleed stream is treated by nanofiltration. Three types of membranes were used in these experiments: 500 and 200 mwco (molecular weight cut off) polyamide and a thin-film composite membrane with 99.2% NaCl rejection. Separation was achieved in two stages. First, separation of sugars was studied with 500 and 200 mwco membranes, and 84% total sugar rejection was obtained. Second, by-products, which constitute the high total organic carbon (TOC) of the wastewater, were separated from the bleed stream by using the thin-film composite membrane. The 95.1% of organics leading to TOC could be removed from the bleed by this method. Based on these results, a waste process, consisting of two nanofiltration units with a 500 mwco membrane and a thin-film composite membrane, were suggested for the recovery of sugars and water.