Algogenic organic matter (AOM) has been extracted from blue-green algae (cyanobacteria) by various means and analyzed by UV absorbance scanning, HPSEC-UV-fluorescence-DOC, FTIR, and fluorescence excitation emission matrix (EEM). AOM extracted in water as a solvent showed a high hydrophilic fraction (57.3%) with a low SUVA (1.0 L/m-mg). The molecular weight (MW) distribution showed a significant heterogeneity (high value of polydispersivity) and high protein content (as indicated by specific fluorescence). A significant amount of proteinaceous components such as mycosporine-like amino acids (MAAs, UV-screening components) and phycobilins (light-harvesting pigment) was detected by UV/visible absorption. The confirmation of proteins was proven by FTIR (at 1,661 cm-1 and 1,552 cm-1) and EEM spectra (EX: 278-282 nm and EM: 304-353 nm). A bench-scale cross-flow unit, employing a flat-sheet membrane specimen, was used to examine nanofiltration (NF) membrane fouling and removal of natural organic matter (NOM) derived from different blends of Suwannee River humic acid (SRHA) and AOM. The flux decline and organic matter rejection as a function of delivered DOC showed significantly different results depending on the organic matter composition of samples even though the test conditions were the same (organic matter concentration, pH, temperature, inorganic salt composition and concentration, and recovery). A higher flux decline was observed with increasing proportions of AOM. Organic matter rejections also decreased with higher AOM contributions to the samples, indicating that lower MW AOM components were not well rejected by the NF 200 membrane having a 360 dalton molecular weight cutoff (MWCO). However, SRHA that shows a relatively high MW (5,000-1,000 daltons) and high SUVA (7.4 L/m-mg) was preferentially rejected through electrostatic repulsion/size exclusion by the NF 200 membrane, having a high negative charge (zeta potential: -15.6 mV), low MWCO, and relatively low hydrophobicity. Even though the DOC concentration of feed water is a decisive factor for membrane fouling along with membrane properties and operating conditions, the characteristics of organic matter are more influential in fouling potential. Protein-like and polysaccharide-like substances were found as major foulants by FTIR.