•Main mechanisms of NF method and their relevant parameters are summarized.•The removal efficiencies of EDCs and PhACs under various conditions are reported.•The negative and positive influence of NOM on the pollutant removal are discussed.•The full-scale applications of NF built for organic removal are summarized.•Main drawbacks of NF applications for organic matter removal are pointed out. Nanofiltration (NF) has been increasingly applied in municipal water treatment plants because it has a high removal rate of organic pollutants while simultaneously reserving certain amounts of minerals that are beneficial for drinking water. Endocrine-disrupting compounds (EDCs) and pharmaceuticals (PhACs) are two groups of the most detrimental and ubiquitous emerging organic compounds present in natural waters and are not effectively removed by conventional treatments. NF has proven to be a promising technology in removing EDCs and PhACs if membrane materials and operational conditions are appropriately applied. This paper outlines the removal efficiencies and mechanisms of EDCs and PhACs by NF based on the analysis of properties of the compounds and membranes as well as some important impact factors. The factors (pH, ionic strength and divalent cations) with a significant impact on the configuration of organic pollutants and membranes are summarized. In particular, the influences of natural organic matter (NOM), which play a vital role in NF applications, on the removal of pollutants and membrane fouling are discussed in detail. Furthermore, the models, including extended Derjaguin-Landau-Verwery-Overbeek (XDLVO) theory, applied in the prediction of membrane fouling are introduced as well. Finally, the typical cases of NF treatment plants as well as the corresponding details are summarized. The main drawbacks and expectations in membrane applications are also investigated.