Growing interest in nanofiltration for solvent purification requires a fundamental understanding of the physicochemical mechanisms of solute retention in organic solvent nanofiltration. In this study, the retention of a similar series of azo dyes with approximately similar molar mass (around 350 Da) by four nanofiltration membranes was studied. The membranes used are commercially available polymeric nanofiltration membranes with molecular weight cutoff between 150 and 300 Da (DuraMem150, StarMem122, NF270 and Desal-Dk). In order to correlate the retention with the size of the molecules, which is assumed to be one of the main factors that determines the retention, use was made of different parameters for the molecular size: molar mass, the Stokes diameter, the equivalent molar diameter, and the cavity surface in methanol and ethanol. All parameters were calculated by using molecular dynamics simulations. For each size parameter, the correlation with retention in nanofiltration experiments was calculated. For the StarMem122 membrane, zero retentions were observed due to the swelling of the membrane and pore size enlargement in methanol and ethanol. For the three other membranes, a fairly good correlation of the retention with the size could only be observed if the size difference between compounds is sufficiently large. Two other factors were studied by using molecular dynamics, i.e., the polarity of the molecule and the electron density of the molecule. The importance of these factors depends on the structure of the molecule as well as the functional groups of the polymer. A very good correlation has been observed for retention of dyes versus their dipole moment. Finally, the effect of solubility parameters of dyes on their retention did not show any significant effect.