The global demand for clean and potable water continuously increased due to expanding population and pollution. Water contamination by anionic compounds, heavy metals, and other pollutants is growing globally and needs to be investigated to find proper strategies leading to improve water quality and reduce water scarcity. Several processes have been used to purify and renew water, but they each have limitations. Processes using membranes for water purification are promising. They found uses for environmental applications as molecular filters. This review aims to show the performance of molecular dynamics (MD) simulations in membrane technologies to increase the knowledge of membrane-based water purification purposes. Through MD simulations, dynamic and static features of membrane separation systems can be evaluated on the atomic scale. This paper reviews recent developments in membrane-based wastewater treatment giving insights obtained from MD simulations. Also, the basics of MD, properties, mechanisms, and its limitations were discussed.