In this study, commercial nanofiltration membranes (Toray, NF 270, Desal 5 L) were characterized by FT-IR spectroscopy, scanning electron microscope, optical profilometry, contact angle, mechanical strength and zeta potential measurements. Filtration performance tests were conducted with distilled water, MgSO4 solution and synthetic dye solutions, respectively. Among three commercial membranes, Toray membrane was thought to be better one. Additional experiments have been carried out for a more detailed characterization of the selected membrane. Therefore, firstly, flux and removal efficiency was monitored by using dye solutions at different pH values, and then experiments were carried out to observe the effect of different temperatures. Also, another filtration test with NaCl solution were performed for Toray membrane. As the main purpose of this study, it was aimed to establish a significant correlation between the structural properties of membranes and their performances. In the light of the results obtained, it has been observed that the contact angle, mechanical strength and surface roughness values of the membrane significantly affect the membrane performance. It was concluded that the most important parameter in dye removal is the zeta potential. As a result of this work, a data set of commercial membranes were created available to all membrane users.