Water, food and energy are at the core of human needs and there is a boundless complex cycle among these three basic human needs. Ecosystems are in the center of this nexus, since they contribute to the provision of each component, making it imperative to understand the role of ecosystems in securing food, water and energy for human well-being. In this study we aimed to map and assess water provisioning services and associated benefits to support the ecosystem–water–food–energy nexus by taking into account environmental flow requirements for riverine ecosystems using the hydrological model Soil and Water Assessment Tool (SWAT). We developed a framework that includes indicators of renewable water (capacity of ecosystem to provide water) and water use (service flow) and we applied it in the Danube river basin over the period 1995–2004. Water scarcity indicators were used to map the possible water scarcity in the subbasins, and analyze the spatial match of water availability and water use. The results show that modelling is instrumental to perform the integrated analysis of the ecosystem–water–food–energy nexus; and that spatial mapping is a powerful tool to display environmental availability of water provisioning and regulatory services delivered by ecosystems, and can support the nexus analysis.