In times of global environmental change, the sustainability of human– environment systems is only possible through a better understanding of ecosystem processes. An assessment of anthropogenic environmental impacts depends upon monitoring natural ecosystems. These systems are intrinsically complex and dynamic, and are characterized by ecological gradients. Remote sensing data repeatedly collected in a systematic manner are suitable for describing such gradual changes over time and landscape gradients, e.g., through information on the vegetation’s phenology. Specifically, imaging spectroscopy is capable of describing ecosystem processes, such as primary productivity or leaf water content of vegetation. Future spaceborne imaging spectroscopy missions like the Environmental Mapping and Analysis Program (EnMAP) will repeatedly acquire highquality data of the Earth’s surface, and will thus be extremely useful for describing natural ecosystems and the services they provide. In this conceptual paper, we present some of the preparatory research of the EnMAP Scientific Advisory Group (EnSAG) on natural ecosystems and ecosystem transitions. Through two case studies we illustrate the usage of spectral indices derived from multi-date imaging spectroscopy data at EnMAP scale, for mapping vegetation gradients. We thus demonstrate the benefit of future EnMAP data for monitoring ecological gradients and natural ecosystems.