Water scarcity is a severe problem for regional environmental protection and socioeconomic development, and water footprints are effective tools for evaluating the magnitude of the water scarcity. However, water is closely intertwined with energy. Carbon taxes are an essential policy tool for managing energy use, and could therefore indirectly change the water footprint. Previous research on water footprints has revealed the historical characteristics of water footprints, but has not predicted how these characteristics would change under a carbon tax. Identifying the indirect impacts of carbon taxes on water footprints could therefore offer important information to support more effective energy and water policies. In the present study, we explored the impacts of carbon taxes on water footprints. We established a computable general equilibrium model to predict the effects of carbon taxes on the socioeconomic system, and adopted an input-output model to account for changes in the water footprint. We then used China as a case study. We found that a carbon tax could reduce the total water footprint, even though the water footprint for primary industries increased. In addition, the tax could decrease the virtual water content, and the reduction of virtual water content is the greatest for the secondary industries.