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Water slip at solid surfaces is important for a wide range of micro/nano-fluidic applications. While it is known that water slip behavior depends on surface functionalization, how it impacts the molecular level dynamics and mass transport at the interface is still not thoroughly understood. In this paper, we use nonequilibrium molecular dynamics simulations to investigate the slip behavior of water confined between gold surfaces functionalized by self-assembled monolayer (SAM) molecules with different polar functional groups. We observe a positive-to-negative slip transition from hydrophobic to hydrophilic SAM functionalizations, which is found related to the stronger interfacial interaction between water molecules and more hydrophilic SAM molecules. The stronger interaction increases the surface friction and local viscosity, making water slip more difficult. More hydrophilic functionalization also slows down the interfacial water relaxation and leads to more pronounced water trapping inside the SAM layer, which both impede water slip. The results from this work will provide useful insights to the understanding of the water slip at functionalized surfaces and design guidelines for various applications.