This study examined the relationship between molecular properties and the fate of trace organic contaminants (TrOCs) in the aqueous and solid phases during wastewater treatment by MBR. A set of 29 TrOCs was selected to represent pharmaceuticals, steroid hormones, phytoestrogens, UV-filters and pesticides that occur ubiquitously in municipal wastewater. Both adsorption and biodegradation/transformation were found responsible for the removal of TrOCs by MBR treatment. A connection between biodegradation and molecular structure could be observed while adsorption was the dominant removal mechanism for the hydrophobic (logD > 3.2) compounds. Highly hydrophobic (logD > 3.2) but readily biodegradable compounds did not accumulate in sludge. In contrast, recalcitrant compounds with a moderate hydrophobicity, such as carbamazepine, accumulated significantly in the solid phase. The results provide a framework to predict the removal and fate of TrOCs by MBR treatment.