This study analyzed the vertical distribution of gravimetric water content (GWC), relative water content (RWC), and equivalent water thickness (EWT) in winter wheat during heading and early ripening stages, and evaluated the position of leaf number at which Vegetation Indexes (VIs) can best retrieve canopy water-related properties of winter wheat. Results demonstrated that the vertical distribution of these properties followed a near-bell-shaped curve with the highest values at the intermediate leaf position. GWC of the top three or four leaves during the heading stage and the top two or three leaves during the early ripening stage can represent the GWC of the whole canopy, but the RWC and EWT of the whole canopy should be calculated based on the top four leaves. At leaf level, the analysis demonstrated strong relationships between EWT and VIs for the top leaf layer, but for GWCD, GWCF, and RWC, the strongest relationships with VIs were found in the intermediate leaf layers. At canopy level, VIs provided the most accurate estimation of GWCfor the top three or four leaves. Water absorption-based VIs could estimate canopy EWT of winter wheat for the top four leaves, but the suitable bands sensitive to water absorptions should be carefully selected for the studied species.