The aim of this study was to assess the impact of caustic cleaning on the rejection of three different trace organic chemical (TrOC) groups (i.e. neutral hydrophilic, neutral hydrophobic and negatively charged) by two nanofiltration (NF) membranes ‒ namely NF270 and NF90. Chemical cleaning was simulated by exposing virgin membrane samples to commercial caustic cleaning formulations as well as sodium hydroxide solutions containing analytical grade additives such as sodium dodecyl sulfate or ethylenediaminetetraacetic acid. The membrane average pore size before and after exposure to a commercially available caustic cleaning formulation was determined based on the pore transport model. The results show that caustic chemical cleaning could cause an increase in the membrane pore size, leading to an increase in permeability and decrease in rejection of conductivity. The impact of caustic cleaning on the pore size and solute rejection was a function of the membrane active skin layer and the chemistry of the cleaning formulation. Caustic cleaning led to a small increase in pore size of the NF270 membrane and resulted in a notable increase in the permeability and salt passage. By contrast, the impact on the NF90 membrane was negligible. The influence of caustic cleaning on TrOC rejection was dependent on physical characteristics of each TrOC including their molecular size, charge, and hydrophobicity. The rejection of neutral and hydrophobic TrOC by the NF270 membrane decreased significantly after exposure to caustic cleaning formulation. However, because the rejection of negatively charged TrOC is governed mostly by electrostatic interaction, their rejection was not significantly affected by caustic cleaning.