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Coupled human and natural system research is an urgent issue in the Anthropocene. However, this has not yet been conducted from the perspective of multiplex networks, which are a powerful tool to elucidate the interactions in human-natural systems. This paper establishes a framework of human-water multiplex networks (HWMNs) to explain the combined effects of human-water interactions in the Yangtze River basin. The spatial linkages and the status of each province in the Yangtze River basin can be characterized through the index of network flow and topology. Research demonstrated that the highest import flow of the virtual water environment capacity flow in the Yangtze River Basin is to Jiangsu Province, at 16.2 thousand t. The highest export flow in the Yangtze River Basin is from Shanghai city, at 33.2 thousand t. The control power of Shanghai city over Sichuan Province accounts for 56.59% of the water resources, which is the highest value and can be recognized as one type of telecoupling of water resources. The provinces in the delta of the Yangtze River basin, including Shanghai city, Jiangsu Province and Zhejiang Province, benefit the most from economic trade. The community structure of the virtual water environment capacity flow is highly consistent with the geographical distribution of the Yangtze River basin. Comprehensive research methods combined with network flow analysis and network topology analysis provide more general results. The microenvironmental effect of indirect pollutant discharge is uncovered through HWMNs. This research can provide a more connected view of integrated water management. Image 1 • A framework of HWMN is established to reveal the combined environmental effects. • The key provinces are revealed through the network flow analysis and topology analysis. • The provinces in the Yangtze river delta obtains most of the water environment benefits. • The environmental effect of the indirect pollutant discharge through HWMN is revealed. [ABSTRACT FROM AUTHOR]