To avoid the re-degradation of repaired regions and ensure the service lives of infrastructures, cementitious materials used for repair applications should possess excellent water penetration resistance. Organic polymers are widely used to enhance water resistance. In this study, the microstructural properties and water uptake of a cementitious material containing a newly developed water-dispersible polyurethane (PU) polymer were investigated. The results showed that the water uptake decreased significantly in the presence of PU. Microscopic observations and gas sorption isotherms indicated that submillimeter and capillary pores and the surfaces of calcium silicate hydrate were partially hydrophobized and/or blocked upon PU addition, which could contribute to the prevention of liquid water uptake. Nevertheless, based on a drying procedure performed prior to the water penetration tests, the specimens with and without PU exhibited similar water vapor uptakes owing to the eliminated difference in the volumes of their micro- and mesopores.