Nitrate (NO3(-)) contamination of freshwater is considered one of the most prevalent global environmental problems. Dual stable isotopic compositions (δ(15)N and δ(18)O) of NO3(-) can provide helpful information and have been well documented as being a powerful tool to track the source of NO3(-) in freshwater ecosystems. The ion-exchange method is a reliable and precise technique for measuring the δ(15)N and δ(18)O of NO3(-) and has been widely employed to collect NO3(-) from freshwater ecosystems. This review summarizes and presents the principles, affecting factors and corresponding significant improvements of the ion-exchange method. Finally, potential improvements and perspectives for the applicability of this method are also discussed, as are suggestions for further research and development drawn from the overall conclusions.