Water managers around the world face the increasingly challenging task to evaluate the impacts of technological measures and policy mechanisms from the local to the river basin scale. A toolset providing quantitative, actionable information on dependencies and trade-offs between upstream and downstream water users is currently lacking. Yet, any intervention needs to be assessed in terms of consequences for downstream water users. This study evaluates the potential of a tracer-like approach, implemented in the water allocation software WEAP, to quantitatively track return flows and their downstream reuse in the river basin context. The WEAP-Virtual Tracer (WEAP-VT) approach was successfully applied to one of Europe's driest river basins, the Segura River Basin in Spain. For each water demand site, the different original sources of water supply, dependency on upstream return flows, and downstream reuse of its return flow were assessed. Based on these results, agricultural, urban, and environmental water users were evaluated in terms of their suitability for water saving measures and their vulnerability to the reduction in upstream return flows. A scenario analysis simulating the improvement of local efficiency improvements shows that specific irrigation schemes and ecosystems become deprived of water. Hence, efficiency improvement in water-scarce basins should be considered with caution. The demonstrated ability to quantify key water reuse indicators for individual water users and at different aggregation levels makes WEAP-VT a valuable tool to support water resource management decisions.