Two different NF membranes were operated to remove natural organic matter (NOM) originating from Dongbok Lake in Korea. Coagulation/sedimentation and sand filtration treated waters as membrane feed waters were used. The tested NF membranes were autopsied to compare the fouling propensity from different feed waters using pure water and a NaOH solution. Organic/inorganic foulants onto membrane surface were analyzed in terms of molecular weight (MW) distribution, structure, and IR analysis, and fouled membranes were also characterized in terms of pore size distribution, surface charge, and SEM-EDS analysis. Polysaccharides and/or N-acetyl aminosugar groups with MW ranging from 30,000 to 50,000 g/mol were identified using HP-SEC and IR analysis. Inorganic foulants (i.e., Si and Al) were also fouled onto the membrane surface and/or pores, and it is effectively removed by caustic cleaning, not pure water. Caustic cleaning was proven to be effective to remove both fouled NF membranes as a basis of flux recovery, and it could efficiently desorb the hydrophobic NOM constituents or protein-like substances from the relatively hydrophilic and less negatively charged NF membranes.