To comprehensively investigate the correlation between free volume properties (size and distribution) in the interior of polyamide (PA) active layer and mass transport mechanism, six polyamide thin film composite (TFC) membranes were characterized using positron annihilation lifetime spectroscopy (PALS). In case of pressurized filtration conditions, the rejection rate of boron across all PA membranes was found to be inversely proportional to the free volume size. The more boron transport occurred at the membrane containing larger free volume. In addition, the transition of the neutral boron transport mechanism from convection to diffusion was found to occur at a membrane free volume radius around 0.275 nm within the applied pressure range (2 and 10 bar), as verified by PALS and the dimensionless Peclet number. We believe that mass transport mechanism transition from convection to diffusion is caused by the compression of polyamide active layer due to applied hydraulic pressure (10 bar), resulting in lowering the convective mass transport pathway inside polyamide active layer. These membrane free volume size criteria and experimental filtration results may subsequently be used as new design guidelines for the development of high boron rejection polyamide TFC membranes having a low energy consumption.