Green roof systems are regarded as a viable solution for mitigating urban environmental challenges and offering a multitude of environmental benefits. Currently, green roofs are increasingly being utilized for the management of rainwater runoff and wastewater. The integration of decentralized rainwater and sewage on-site treatment technology with urban green buildings is being gradually promoted. Green roofs can also be considered as a form of decentralized rainwater and sewage on-site technology, which holds great potential for widespread adoption in the future. Several studies have suggested that green roofs may serve as a potential source of pollutants; however, there are also studies that clearly demonstrate the efficient removal of nutrients and organic pollutants by green roofs. This article critically examines the existing literature on water treatment aspects associated with green roofs and elucidates their classification and operational mechanisms. Through an analysis of previous research cases, it becomes evident that both substrate and vegetation play a significant role in influencing the treatment performance of green roofs. By designing and configuring appropriate substrate and vegetation, green roofs can play a pivotal role in the purification of water quality. Finally, a brief outlook is presented for the future research directions of green roofs, with the anticipation that green roofs will feature more innovative and environmentally friendly designs, as well as expanded prospects for application.