Aquaporins (AQPs) are a family of water channels predominantly expressed on cell membranes. They are widely distributed throughout the human body and play crucial roles in multiple biological processes, such as homeostasis maintenance. Additionally, AQPs are actively involved in the pathophysiological processes of neurological disorders. They are closely associated with fluid movement, cerebrospinal fluid circulation, energy metabolism, signal transduction, neurogenesis, neural regeneration, and the development and stabilization of the blood-brain barrier within the central nervous system (CNS), contributing to the onset and progression of various CNS diseases, including cerebral edema, Alzheimer's disease, neuromyelitis optica, intracranial hypertension, and Parkinson's disease. So far, multiple types of AQPs have been identified in the CNS, with research attention mainly devoted to AQP1, AQP4, and AQP9. The study of AQPs is instrumental in deepening our understanding of CNS and providing potential therapeutic targets for associated diseases. This article demonstrates the physiological distribution of AQPs in the CNS, their regulatory mechanisms, physiological functions, and their associations with CNS diseases, offering novel insights for relevant neuroscientific research.