Comparison of nanofiltration characterization data from literature is challenging due to different hydrodynamics and system designs, which affect membrane retention. In this study, stirred cell (SC), micro and macro cross flow systems (micro and macro CF) with different configuration were used to measure salt and organic tracer retention. Minimal concentration polarization conditions were applied in order to: 1) evaluate comparability of the systems for characterization of membrane pore radius and molecular-weight-cut-off, 2) understand the impact of system configuration and operation on mass transfer, 3) compare salt retention at laboratory scale with the retention of spiral wound module. Results indicated that system dimension was the most important parameter to affect the mass transfer and the concentration of both salt and organic tracers on the membrane surface (C-m) in the macro CF system. Indeed, the higher channel length to width ratio of macro CF was related to reduced mass transfer and higher C-m. However, a comparability of the three systems was observed by operating at low flux (below 80 L/m(2)h) and higher cross flow velocity (above 0.4 m/s), where the lowest concentration polarization conditions were maintained. This is valid taking into account the variation of hydrodynamics (e.g. relation of Sherwood number and Reynolds range), which is intrinsically related to the different operation modes of dead end and cross flow. This study gives a novel contribution to improve the accuracy of membrane characterization methodologies and to identify suitable operative conditions for testing new membrane materials at small scale.