Perchlorate and tris(2-chloroethyl) phosphate (TCEP), which have been widely detected micropollutants in rivers and wastewater effluents, were investigated in terms of removals by nanofiltration (NF) membranes under different membrane feed water conditions. For this study, NF membranes with different characteristics, including molecular weight cutoff (MWCO), relative hydrophobicity, and roughness, were used. To demonstrate the effect of electrostatic repulsion between the membrane surface and investigated compounds, the conductivity of membrane feed solutions were altered using sodium chloride; the effects of natural organic matters on removal efficiencies of tested compounds were also demonstrated using synthetic model solutions and the Youngsan River water. Filtration tests with seawater were conducted to investigate applicability of NF membranes for desalination. A relatively loose NF membrane with lower hydrophobicity and lower roughness exhibited lower removal efficiencies for both perchlorate and TCEP than the other tight NF membranes with lower MWCO. When comparing removal efficiencies of perchlorate and TCEP for the loose NF membrane, removals of uncharged TCEP were less affected by differences in solution chemistry variations than those of perchlorate. The tight NF membranes exhibited higher removal efficiencies for both perchlorate and TCEP than the loose NF membrane, as expected, under tested conditions, including seawater.