Two kinds of newly designed feed channels, for example, a spiral and a serpentine feed channels, for a bench-scale nanofiltration module were developed to improve the filtration performance. The experiments were carried out with the modules using a commercial flat NF membrane to investigate the effects of Reynolds number (Re) and flow channel structures on the flux of permeate and Mg2+ rejection. It was shown from the experimental results that although the effects of Reynolds number on fluxes were not obvious for the two new feed channels compared with a normal flow channel structure, the Mg2+ rejections varied apparently with Re. The Mg2+ rejections were almost the same for the modules with two new feed channels and larger than that for the module with normal feed channel. The numerical simulations of fluid flow in the three kinds of feed channels were completed at Re of 4800 to explain the phenomena. The results demonstrated that there was a secondary flow in both new feed channels, which strongly influences the Mg2+ rejection. The rejection increased with increasing average shear stress at the membrane wall. The spiral feed channel was the best one among the flow channel structures investigated.