This study examined the relationship between specific molecular features of trace organic contaminants and their removal efficiencies by a laboratory scale membrane bioreactor (MBR). Removal efficiencies of 40 trace organic compounds were assessed under stable operating conditions. The reported results demonstrate an apparent correlation between chemical structures and the removal of trace organic contaminants by the laboratory scale MBR system. The removal of all 14 very hydrophobic (Log D > 3.2) trace organic compounds selected in this study was consistently high and was above 85%. The occurrence and types of electron withdrawing or donating functional groups appear to be important factors governing their removal by MBR treatment. In this study, all hydrophilic and moderately hydrophobic (Log D < 3.2) compounds possessing strong electron withdrawing functional groups showed removal efficiency of less than 20%. In contrast, high removal efficiencies were observed with most compounds bearing electron donating functional groups such as hydroxyl and primary amine groups. A qualitative framework for the assessment of trace organic removal by MBR treatment was proposed to provide further insights into the removal mechanisms.