This study aimed to elucidate key factors governing the rejection of trace organic contaminants (TrOCs) by nanofiltration (NF) and reverse osmosis (RO) membranes. The rejection of 16 selected hydrophilic and hydrophobic TrOCs by an NF and an RO membranes was evaluated at different solution pH values using a cross-flow NF/RO filtration system. An analytical technique consisting of solid phase extraction followed by gas chromatography and mass spectrometry detection was used for the analysis of the TrOCs. In general, rejection increased in the order of decreasing membrane permeability, increasing molecular weight (or equivalent molecular width) of the TrOCs, and increasing hydrophilicity. Adsorption of hydrophobic TrOCs to the membrane could be observed based on a mass balance calculation. However, the correlation between adsorption and log D value (the logarithm of the octanol-water distribution coefficient) of the TrOCs (which indicates their hydrophobicity) observed in this study was rather weak. This is due to the adsorption being not only dependent on hydrophobicity, but also on other physicochemical aspects of TrOCs and the membrane material, such as molecular size, charge of the compounds, pore size, charge, and surface roughness properties of the membranes. Therefore, the results suggest that these factors may also govern the adsorption (and subsequently rejection) of TrOCs to NF/RO membranes.