Nanofiltration membranes (NF) have applications in several areas. One of the main applications has been in water treatment for drinking water production as well as wastewater treatment. NF can either be used to treat all kinds of water including ground, surface, and wastewater or used as a pretreatment for desalination. The introduction of NF as a pretreatment is considered a breakthrough for the desalination process. NF membranes have been shown to be able to remove turbidity, microorganisms and hardness, as well as a fraction of the dissolved salts. This results in a significantly lower operating pressure and thus provides a much more energy-efficient process. Similar to other membrane processes, a major problem in NF membrane applications is fouling. Several studies have investigated the mechanisms of fouling in NF membranes and suggested methods to minimize and control the fouling of NF membranes. For NF membrane characterizations and process prediction, modeling of NF processes and the use of atomic force microscopy (AFM) are very important. The ability to predict the performance of NF processes will lead to a lower number of experiments, saving of time and money, and help to understand the separation mechanisms during NF. A comprehensive review of NF in water treatments is presented including a review of the applications of NF in treating water as well as in the pretreatment process for desalination; the mechanism as well as minimization of NF membrane fouling problems; and theories for modelling and transport of salt, charged and noncharged organic compounds in NF membranes. The review will also address the application of AFM in studying the morphology of membrane surfaces as part of the NF membrane characterization.