The desalination of model solutions containing iminodiacetic acid (IDA) and NaCl was examined using three commercial nanofiltration (NF) membranes (NF270, Desal-5 DL, Nanomax50). Experimental results showed that with all the three membranes, the rejection of IDA increased with the increase of pH from 8 to 11, and negative rejection of Cl− was found in filtration in a certain range of pH. NF270 was chosen to further investigate the effect of permeate flux, temperature and solutes concentration on the separation of IDA and NaCl. The results showed that IDA rejection decreased with the increase of temperature and salt concentration, and the high concentration of IDA could induce a lower rejection of NaCl. Furthermore, the desalination and recovery were examined with model solution in different operation modes and a laboratory scale test with an industrial fluid was also performed. Under suitable conditions, with NF270, the recovery of IDA could be more than 95% while the NaCl removal was greater than 58%.