Aquaporins (AQPs) are water channel proteins facilitating passive transport of water and other small molecules across biomembranes. Regulation of osmotic homeostasis via AQPs is accompanied by dynamic participation of various cellular signaling pathways. Recently emerging evidence reveals that functional roles of AQPs are further extended from the osmotic regulation via water permeation into the cell proliferation and differentiation. In particular, anomalous expression of AQPs has been demonstrated in various types of cancer cells and cancer stem-like cells and it has been proposed as markers for proliferation and progression of cancer cells. Thus, a more comprehensive view on AQPs could bring a great interest in the cell stemness accompanied by the expression of AQPs. AQPs are broadly expressed across tissues and cells in a cell type- and lineage-specific manner during development via spatiotemporal transcriptional regulation. Moreover, AQPs are expressed in various adult stem cells and cells associated with a stem cell niche as well as cancer stem-like cells. However, the expression and regulatory mechanisms of AQP expression in stem cells have not been well understood. This review highlighted the AQPs expression in stem cell niches/stem cells and the involvement of AQPs in the cell proliferation and signaling pathways associated with cell stemness.