We report the molecular dynamics simulations of spontaneous and continuous permeation of water molecules through a single-layer graphyne-3 membrane. We found that the graphyne-3 membrane is more permeable to water molecules than (5, 5) carbon nanotube membranes of similar pore diameter. The remarkable hydraulic permeability of the single-layer graphyne-3 membrane is attributed to the hydrogen bond formation, which connects the water molecules on both sides of the monolayer graphyne-3 membrane and aids to overcome the resistance of the nanopores, and to the relatively lower energy barrier at the pore entrance. Consequently, the single-layer graphyne-3 membrane has a great potential for application as membranes for desalination of sea water, filtration of polluted water, etc.