Optimal conditions of ultrafiltration (UF) and nanofiltration (NF) were investigated for separation and concentration of isoflavones and oligosaccharides from Sunmul. Levels of COD, BOD, and suspended solids (SS) in UF and NF permeates were also determined to evaluate effectiveness of these processes for reducing water pollution. Optimal UF operation conditions to achieve minimal fouling and maximal flux were $33-34^{circ}C$ operating temperature and 2.3-2.4 bar trans-membrane pressure. Recovery yields of isoflavones and oligosaccharides in UF retentate were 11.49-28.16% and 12.77-27.57%, respectively. Increase in volumetric concentration factor (VCF) resulted in more functional compounds of isoflavones and oligosaccharides passing through UF membrane. Total isoflavone and oligosaccharide yields decreased by 3% as VCF increased from 6.0 to 8.0 and from 8.0 to 10.0, while decreased significantly by 10% as VCF decreased from 4.0 to 6.0. Optimal NF operating conditions were 192-195 psig operating pressure at $30-33^{circ}C$. Total yields of isoflavones and oligosaccharides significantly decreased at VCF 8.0, whereas did not decrease up to VCF 6.0 during NF operation. Therefore, VCF 6.0 was recommended for economical process. COD and BOD decreased by more than 98% after NF process, and SS were not detected after UF process. These results indicated sequential filtration process was useful for separation of isoflavones and oligosaccharides from Sunmul and for reducing water contaminants.