The effects of controlled temperature variation in the range of 10–45 °C were assessed in a lab-scale MBR that treated synthetic municipal wastewater spiked with selected micropollutants. The effects were evaluated with respect to total organic carbon (TOC) and total nitrogen (TN) removal, micropollutant removal, sludge growth, level of soluble microbial products (SMPs) in the mixed liquor and membrane fouling. Overall, the temperature shifts caused high variation in the TOC and TN levels in the reactor supernatant, however that in membrane-permeate was relatively more stable, substantiating the robustness of the MBR process. Results regarding the removal of micropollutants at ambient temperature (20 °C) demonstrate an apparent correlation between hydrophobicity, chemical structures and the removal of micropollutants. Temperature variation below and above 20 °C, especially the operation under 45 °C appeared to significantly influence the removal of certain less hydrophobic (log D < 3.2) micropollutants possessing strong electron withdrawing functional groups. The removal of most hydrophobic compounds (log D > 3.2) was stable under the temperature range of 10–35 °C, however, deteriorated at 45 °C. The temperature shifts were also associated with higher levels of SMP in the mixed liquor which appeared to trigger membrane fouling as evidenced by a rapid increase in transmembrane pressure.