Virtual water exerts an essential effect on water resources, yet such effect is rarely considered in current studies on water rights allocation in transboundary rivers. Hence, this paper ran a case study on Taihu Lake Basin, collecting data from 2017 to make clear the physical water rights of four regions—Jiangsu Province, Zhejiang Province, Anhui Province, and Shanghai City—in the Basin. After that, the multiregional input–output (MRIO) approach was utilized to measure the trade in value-added (TiVA) transfer and virtual water transfer (VWT) and construct an inequality index of VWT (VWI). Next, water efficiency coefficient was employed to convert the VWT into riparian level. Finally, VWT and VWI were incorporated into the water rights allocation model to form up a water rights allocation scheme for Taihu Lake Basin. Results showed: (1) Jiangsu enjoys the most allocated physical water rights, followed by Zhejiang, and Anhui ranks the lowest; (2) Anhui and Jiangsu are net virtual water exporters (2.259 billion m3 and 1.78 billion m3, respectively), while Zhejiang and Shanghai are net importers (2.344 billion m3 and 1.695 billion m3, respectively); (3) Anhui suffers the most inequality—0.4401—followed by 0.5076 of Jiangsu, while Zhejiang has the most equal environment—0.7012; (4) after the inclusion of virtual water, the quantity of water rights allocation changes, whereas Anhui experiences the largest growth—144 million m3—due to the dual effects from the highest VWT and inequality. In conclusion, the effect of virtual water is indispensable, so VWT and VWI should both be considered in the physical water rights allocation of transboundary rivers.

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