Metal-organic frameworks (MOFs) are significantly tunable materials that can be exploited in a wide range of applications. In recent years, a large number of studies have been focused on synthesizing nano-scale MOFs (nanoMOFs), thus taking advantage of these unique materials in various applications, especially those that are only possible at nano-scale. One of the technologies where nanoMOF materials occupy a central role is the membrane technology as one of the most efficient separation techniques. Therefore, numerous reports can be found on the enhancement of the physiochemical properties of polymeric membranes by using nanoMOFs, leading to remarkably improved performance. One of the most considerable applications of these nanoMOF-based membranes is in water treatment systems, because freshwater scarcity is now an undeniable crisis facing humanity. In this in-depth review, the most prominent synthesis and post-synthesis methods for the fabrication of nanoMOFs are initially discussed. Afterwards, different nanoMOF-based composite membranes such as thin-film nanocomposites (TFN) and mixed-matrix membranes (MMM) and their various fabrication methods are reviewed and compared. Then, the impacts of using MOFs-based membranes for water purification through growing metal-organic frameworks crystals on the support materials and utilization of metal-organic frameworks as fillers in mixed matrix membrane (MMM) are highlighted. Finally, a summary of pros and cons of using nanoMOFs in membrane technology for water treatment purposes and clear future prospects and research potentials are presented.