Dissolved organic nitrogen (DON) measurements for water samples with a high dissolved inorganic nitrogen (DIN, including nitrite, nitrate and ammonia) to total dissolved nitrogen (TDN) ratio using traditional methods are inaccurate due to the cumulative analytical errors of independently measured nitrogen species (TDN and DIN). In this study, we present a nanofiltration (NF) pretreatment to increase the accuracy and precision of DON measurements by selectively concentrating DON while passing through DIN species in water samples to reduce the DIN/TDN ratio. Three commercial NF membranes (NF90, NF270 and HL) were tested. The rejection efficiency of finished water from the Yangshupu drinking water treatment plant (YDWTP) is 12%, 31%, 8% of nitrate, 26%, 28%, 23% of ammonia, 77%, 78%, 82% of DOC (dissolved organic carbon), and 83%, 87% 88% of UV 254 for HL, NF90 and NF270, respectively. NF270 showed the best performance due to its high DIN permeability and DON retention (∼80%). NF270 can lower the DIN/TDN ratio from around 1 to less than 0.6 mg N/mg N, and satisfactory DOC recoveries as well as DON measurements in synthetic water samples were obtained using optimized operating parameters. Compared to the available dialysis pretreatment method, the NF pretreatment method shows a similar improved performance for DON measurement for aqueous samples and can save at least 20 h of operating time and a large volume of deionized water, which is beneficial for laboratories involved in DON analysis. DON concentration in the effluent of different treatment processes at the YDWTP and the SDWTP (Shijiuyang DWTP) in China were investigated with and without NF pretreatment; the results showed that DON with NF pretreatment and DOC both gradually decreased after each water treatment process at both treatment plants. The advanced water treatment line, including biological pretreatment, clarification, sand filtration, ozone-BAC processes at the SDWTP showed greater efficiency of DON removal from 0.37 to 0.11 mg N L −1 than that at the YDWTP, including pre-ozonation, clarification and sand filtration processes from 0.18 to 0.11 mg N L −1.