Watersheds, climate regimes and nature in general do not abide to boundaries created by human institutions, increasing the difficulty for these institutions to manage them. Human activity is, on the other hand, capable of linking geographically separate regions through trade and supply chains. Implementing the water-energyfood nexus therefore often requires science and policy to work on a trans-boundary level. This article looks at two examples of quantitative trans-boundary approaches in science. Johansson explored the effects of foreign land acquisition on regional water scarcity through virtual water flows. The virtual water flows were based on the water used to produce the exported food and energy crops. The flows were aggregated on a national basis to compare countries. Van der Krogt presented a water simulation model for the Eastern Nile Basin, developed through joint cooperation between the four Eastern Nile countries. The model incorporates information on all current, planned and potential water infrastructure and irrigation projects into different scenarios. These are compared with a long term hydrological baseline to assess the impact development has on downstream water supply. This new tool allows Eastern Nile countries to better understand how their actions can affect downstream neighbours.