Abstract Water is essential for bioenergy production. Characterized as low carbon technology, crop-based bioenergy technology witnesses rapid development, inevitably putting pressure on global water resources. Therefore, it is crucial to carefully assess bioenergy technology’s overall impact on scarce water source for a sustainable bioenergy future. In this regard, this study aims to evaluate the life cycle water use of bioenergy from agricultural residues via the first pilot moving-bed pyrolysis polygeneration system in China. By using a tiered hybrid life cycle assessment, both direct and indirect water use are calculated. Results show life cycle water use is 3.89 L H2O/MJ and agricultural process dominates the total water use. Scenarios analysis shows different feedstock allocation ratios during agricultural production have striking influence on water use intensity. In addition, the choice of feedstock is another important influential factor. Under the 2020 Scenario in China’s 13th Five Year Plan, if all the bioenergy target could be met by polygeneration the estimated annual water use will be 6.6 billion m3, in magnitude up to around ten times the total water consumption in Denmark in 2013. In global scenario of potential feedstock available in 2060, the estimated water use for bioenergy produced by polygeneration will be 179–369 billion m3. Although the water use intensity of bioenergy production from agricultural residues by polygeneration is lower than that for other biomass conversion pathways, it is still higher than water intensity of conventional fossil energy products. Large-scale bioenergy production will have macroscopic effects on water demand. Finally, suggestions such as selecting high water-efficient biomass feedstock and reinforcing water-saving irrigation management to minimize water use in agriculture stage are proposed.