Separation of organic compounds from aqueous streams presents many challenges regarding materials and separation conditions. Such separations become increasingly important with the development of biomass related processes. Pervaporation is a promising membrane process capable of isolating organic species from aqueous feeds. Typically, volatile organic compounds (VOCs) removal from water suffers from mass transport limitations due to depletion of the minor component at the membrane surface. Understanding of such mass transport limitations is crucial for the development of novel pervaporation membranes and methods. In this work, we present a performance study on the removal of trace amount of acetone from water via pervaporation to provide insight on mass transport limitations. We used glass microfluidics containing a thin polydimethylsiloxane (PDMS) membrane that allows very fast removal of acetone from water. Via modelling and experiments, we quantitatively investigate the mass transfer coefficients of acetone through the liquid boundary layer (klkl) and that of the membrane (kmkm) by varying membrane thicknesses and feed flow rates. High acetone removal efficiency of 81% is achieved for just 3 min residence time at room temperature for a 35 μm thin membrane. A design criterion based on intrinsic system parameters is derived to engineer the pervaporation system for both micro- and macro-scales. Our micro-PV device shows promising potential regarding the characterisation of pervaporation processes and materials for the removal of VOCs from water.