Nanofiltration membranes have been characterized by computer controlled permeation experiments to provide certified results. This method records a real-time history of operating conditions and allows the incorporation of variations in the calculations of derived parameters. The effects of temperature and physical properties of feed on permeation have been evaluated and incorporated in models describing fluid flow trough membranes. As the influence of initial experimental conditions in nanofiltration is very significant, a method based on system mass-transfer coefficient is proposed in order to verify the accuracy of the results.