A globally imminent shortage of freshwater has been demanding viable strategies for improving desalination efficiencies with the adoption of cost- and energy-efficient membrane materials. The recently explored 2D transition metal dichalcogenides (2D TMDs) of near atomic thickness have been envisioned to offer notable advantages as high-efficiency membranes owing to their structural uniqueness; that is, extremely small thickness and intrinsic atomic porosity. Despite theoretically projected advantages, experimental realization of near atom-thickness 2D TMD-based membranes and their desalination efficiency assessments have remained largely unexplored mainly due to the technical difficulty associated with their seamless large-scale integration. Herein, we report the experimental demonstration of high-efficiency water desalination membranes based on few-layer 2D molybdenum disulfide (MoS2) of only ∼7 nm thickness. Chemical vapor deposition (CVD)-grown centimeter-scale 2D MoS2 layers were integrated onto porous polymeric supports with well-preserved structural integrity enabled by a water-assisted 2D layer transfer method. These 2D MoS2 membranes of near atomic thickness exhibit an excellent combination of high water permeability (>322 L m-2 h-1 bar-1) and high ionic sieving capability (>99%) for various seawater salts including Na+, K+, Ca2+, and Mg2+ with a range of concentrations. Moreover, they present near 100% salt ion rejection rates for actual seawater obtained from the Atlantic coast, significantly outperforming the previously developed 2D MoS2 layer membranes of micrometer thickness as well as conventional reverse osmosis (RO) membranes. Underlying principles behind such remarkably excellent desalination performances are attributed to the intrinsic atomic vacancies inherent to the CVD-grown 2D MoS2 layers as verified by aberration-corrected electron microscopy characterization.