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Rejection mechanism of nanofiltration (NF) membrane for organic solutes (including alkyl phenol, bisphenol A, phthalate acid esters, phosphoric acid esters, other plastic additives, and natural hormones like 17β estradiol, etc) was examined. The experiments indicated almost complete removal of these solutes by the tight NF membranes, while the rejection obtained by the loose membranes was dependent on solute species. Compounds with flat-shaped structure like 2-H-benzothiazol and dimethyl phthalate were more permeable than other target solutes within the same molecular size range. Of the four methods of size determination used, there was no significant difference in the accuracy of prediction of rejection from the solute sizes. The size configurations of molecules have been identified to greatly influence the permeation or retention, yet the size parameter was thought to be incomplete as a single parameter in describing rejection of organic solutes. The logarithm of octanol-water partitioning coefficients of solutes appears not to be an effective parameter in modelling rejections as its contribution was only slight or minor. We obtained better correlations with structural configuration of molecules (by molecular width and length) and polarity of the molecules.