Disclosed are vehicle sunroof assemblies with enhanced water management systems, methods for making/using such sunroof assemblies, and vehicles equipped with sunroof assemblies having sunshade water drainage backup capabilities. A representative sunroof assembly includes a frame that attaches to the body of a motor vehicle, positioned within an aperture in the vehicle's roof structure. A center panel is movably mounted to the frame, and operable to transition between open and closed positions to thereby obstruct and expose the aperture. Also attached to the frame is a drain channel that collects and expels fluids from the sunroof assembly. A sunshade is movably mounted to the frame adjacent the center panel. The sunshade manually or automatically transitions between deployed and stowed positions to thereby prevent and allow the passage of light through the roof's aperture. When in the deployed position, the sunshade repels water and directs the repelled water into the drain channel.