Ecological compensation is an effective means to solve the conflict of interests among trans-boundary river basin countries. How to determine the ecological compensation standard is the core of ecological compensation. On the basis of the emergy synthesis method, we developed an emergy-water resources ecological footprint model for trans-boundary river basin countries. Based on the calculation of ecosystem service value and consumption ecological value of trans-boundary river basin countries, the ecological spillover value of each basin country is obtained. From the perspective of supply and consumption, the ecological compensation standard in basin countries is determined by judging the supply and consumption status of ecological services and combining with the willingness to pay for ecological compensation. Taking the Lancang–Mekong River Basin as an example, the results show that (1) the ecosystem service value of the Lancang–Mekong River Basin countries from high to low is Laos, Cambodia, Thailand, China, Vietnam, and Myanmar; (2) in terms of ecosystem service value consumption, the order from high to low is Thailand, Cambodia, Vietnam, China, Laos, and Myanmar; and (3) Thailand and Vietnam, located in the lower reaches of the basin, belong to the consumers of ecological services, and based on the actual willingness to pay, they need to pay $46.913 billion and $1.699 billion, respectively.

The River Chief Policy (RCP) is an innovative water resource management system in China aimed at managing water pollution and improving water quality. Though the RCP has been piloted in some river basins of China, few scholars have studied the effects of the policy. We built a differential game model under random interference factors to compare the water pollution in Chaohu Lake under the RCP and without the RCP, and we explored the conditions to ensure the effectiveness of the RCP. The results showed that: (1) The average effect of water pollution control under the RCP was greater than under non-RCP; (2) the higher the rewarding excellence and punishing inferiority coefficient ( $\theta$ ) was, the better the water pollution control effect under the RCP; (3) the greater the random interference coefficient ( $\sigma$ ) and rewarding excellence and punishing inferiority coefficient ( $\theta$ ) were, the bigger the fluctuation of the water pollution control effect was; (4) when using the stochastic differential game, when $\sigma \le 0.0403$ , $\theta \ge 0.0063$ , or $\sigma >0.0403$ , $\theta \ge 0.268$ , the RCP must be effective for water pollution control. Therefore, we can theoretically adjust the rewarding excellence and punishing inferiority coefficient ( $\theta$ ) and the random interference coefficient ( $\sigma$ ) to ensure the effective implementation of the RCP and achieve the purpose of water pollution control.

With the rapid development of social economy and global climate warming, scarce transboundary water resources, as one of the basic resources for socio-economic development, have increasingly become the focus of basin countries. To investigate the socio-economic impacts of different water diversion quantity from transboundary river basins, we used a system dynamics (SD) model to reflect interactions between population, water resources, and socio-economic development, and applied it to a case study in Xinjiang to simulate its change tendency from 2011 to 2030 from the temporal dimension. Then, four water diversion quantity of transboundary river basins and four alternative socio-economic development patterns were designed to comprehensively evaluate these impacts of water diversion quantity change on the socio-economy of the region along the river under different socio-economic development patterns. The results indicate that (1) there was a positive correlation between water diversion quantity and the economic output value of the region along transboundary river basins, and the marginal benefit of transboundary water resources would decrease gradually; (2) considering the difficulty of water diversion from transboundary river basins and the protection of downstream water use and ecological health of transboundary river basins, we believe that increasing the transboundary water resources by 20% was more conducive to the sustainable development of Xinjiang’s socio-economy; (3) through the comparison of dynamic evolutions of socio-economic development and water impacts under four socio-economic development patterns, it is best for Xinjiang to plan its future development in the coordinated development of economic-resource scenario. Following this scenario, not only would the total output value of the socio-economy be better than other scenarios, but this also helps to alleviate the contradiction between the water supply and demand, which expected there would be a water shortage of 1.04 billion m³ in 2029 under 20% increase in water diversion quantity. Therefore, appropriate water diversion quantity, reasonable adjustment of industrial production growth rate, reduction of water consumption quotas of different industries and domestic water quota, and improvement of collection and treatment rate for sewage should be given priority in water resources management decision-making in Xinjiang or other arid regions along transboundary river basins.

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.

Water stress in countries within a drainage basin exacerbates the water quantity conflict in transboundary rivers. However, few studies considered the invisible effect of virtual water transfer on water quantity conflict by intensifying water stress. Therefore, this study, with Ili River as the case, collects data on Virtual Water Trade (VWT) from 1990 to 2015, uses water stress index (WSI) to assess water stress values under two scenarios (with or without virtual water transfer), and takes Grey Verhulst Model to predict two scenarios water stress values respectively. Next, based on the Levenberg—Marquardt (LM) Algorithm, this study compares the water quantity conflict intensity of the two scenarios, and further explores the invisible effect of virtual water transfer on the conflicts among transboundary rivers. Results show: (1) During the study period (1990–2015), water stress in China and Kazakhstan along the banks of Ili River increased in general. (2) China was basically a net exporter of virtual water during 1990–1995, and Kazakhstan became a net exporter after 1995. (3) During 2020–2025, water conflict value of Ili River without virtual water transfer is 0.458, while the value rises to 0.622 with virtual water transfer, indicating that virtual water transfer between China and Kazakhstan has an invisible enhancement on the water quantity conflict of Ili River. (4) The intensified water quantity conflict is mainly caused by the more and more serious water stress in Kazakhstan. On such basis, it is more urgent for Kazakhstan to restructure its economy and trade.