A membrane-based separation process (nanofiltration) is used to separate dyes from aqueous solution. The selected dyes are crystal violet (molecular weight 408) and methylene blue (molecular weight 373), respectively. An organic membrane with molecular weight cutoff of 400 is used for the experiments. The experiments are conducted in an unstirred batch cell and a rectangular cross-flow cell for single as well as binary dye mixtures. It has been observed that for cross-flow cell, the system reaches steady-state quickly. Separation up to 95% for the single component is achieved. For mixtures, separations up to 60% and 35% of the two dyes are obtained respectively. The separation and fractionation of the dye(s) are studied as functions of operating parameters, e.g., transmembrane pressure, dye concentration in the feed, and cross-flow velocity.