ZnO was deposited on macroporous α-alumina membranes via atomic layer deposition (ALD) to improve water flux by increasing their hydrophilicity and reducing mass transfer resistance through membrane pore channels. The deposition of ZnO was systemically performed for 4–128 cycles of ALD at 170 °C. Analysis of membrane surface by contact angles (CA) measurements revealed that the hydrophilicity of the ZnO ALD membrane was enhanced with increasing the number of ALD cycles. It was observed that a vacuum-assisted ‘flow-through’ evaporation method had significantly higher efficacy in comparison to conventional desalination methods. By using the vacuum-assisted ‘flow-through’ technique, the water flux of the ZnO ALD membrane (~170 L m−2 h−1) was obtained, which is higher than uncoated pristine membranes (92 L m−2 h−1). It was also found that ZnO ALD membranes substantially improved water flux while keeping excellent salt rejection rate (>99.9%). Ultrasonic membrane cleaning had considerable effect on reducing the membrane fouling.