Desalination of iron dextran solution containing a high salt content (≈18% NaCl (w/v)) by nanofiltration (NF) was examined using three commercial nanofiltration membranes (NF270, Desal-5 DL, Nanomax50). With these NF membranes, iron dextran was almost completely rejected, while salt rejection was so small (Robs ≈ −2 to 1.5%) that salt ions could pass through the membranes easily. No irreversible fouling was found for each membrane used and a distinct transmembrane pressure (TMP) drop appeared during diafiltration at a flux of 15.5 L m−2 h−1 (20 °C). And the weakening of concentration polarization (CP) of iron dextran was thought to be the possible reason for TMP drop. It was found that with the decrease of salt concentration, the viscosity of solution decreased, thus enhancing the back transport of iron dextran molecules. As a result, the concentration of iron dextran at membrane surface and filtration resistance could be reduced. However, this effect showed a little hysteresis due to the high viscosity of the feed, the pump pulse or pause would counteract the hysteresis by promoting the molecule to redisperse. Flux history had a strong influence on CP of iron dextran because of shear-enhanced diffusion. Furthermore, the effect of flux, stirring speed, and temperature on CP of iron dextran was also examined in “total recirculation” experiments. These results from the laboratory-scale tests could serve as valuable guide for process design in industrial production.