Current studies neglect how virtual water transfer (VWT) between countries within a drainage basin affects water stress and then yields an invisible effect on the water quantity conflict in transboundary rivers, which would further make management policies on water quantity conflict less fair and reasonable. Therefore, this study first constructs the Inequality Index of VWT and water stress index (WSI) to assess water stress. Next, different types are set according to the Inequality Index and WSI to analyze management policies, with Ili River as the case. Results show: (1) Within the study period, from 1996, the Inequality Index of VWT between China and Kazakhstan stayed at 0.368 (0.368 < 0.5), indicating a relatively high inequality of VWT between the two countries—China at a disadvantage, while Kazakhstan having the upper hand. (2) According to the remotely sensed data, WSI in the riparian zones of the Ili River rose from 0.288 to 0421 in China, and 0214 to 0.402 in Kazakhstan, showing intermediate scarcity. (3) China and Kazakhstan both fall into Type 2, and Kazakhstan has the advantageous position. Therefore, while allocating the water resources of the Ili River, Kazakhstan should lower its expectation and proactively ask to exchange benefits in other aspects to reverse the outward transfer of its physical water. In addition, the two countries should find suitable ways to go about water rights trading to reduce the possibility of potential water quantity conflict.

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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.

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The ecological compensation standard in transboundary river basins should be determined by the basin countries through negotiation on the basis of the base value of the ecological compensation standard. This paper calculated the base value range of the ecological compensation standard, determining the upper limit based on the spillover value of ecosystem services for the ecosystem-service-consuming country and the lower limit according to the cost of ecological protection for the ecosystem-service-supplying country. The final range was determined by integrating this with the willingness to pay and the actual effort in each basin country. Taking, for example, the Lancang–Mekong River basin, the results indicate that the spillover value of ecosystem services in Laos, China and Myanmar was positive and these three countries were ecosystem-service-supplying countries, while in Cambodia, Vietnam and Thailand it was negative and these three countries were ecosystem-service-consuming countries. Among the ecosystem-service-supplying countries, the cost of ecological protection of them was in descending order of Laos, China and Myanmar, which was related to their own level of economic development. Considering the adjustment coefficient for the payment of ecosystem service value and the cost-sharing coefficient of each basin country, the feasible range for the base value of the ecological compensation standard was determined to be [2.47, 229.67] × 108 $, which provided the basis for the negotiation on the determination of the ECS. In addition, implementation suggestions were proposed from three aspects: establishing a basin-information-sharing mechanism and platform, establishing an integrated management organization for transboundary river basins, and strengthening and improving the coordination and supervision model of ecological compensation.