Hydroelectric power is a popular alternative to burning fossil fuels, especially within the Amazon river basin. However, no single hydropower installation is without any environmental impact. By damming a river, significant alterations do occur in the hydrological connectivity, which reverberate in the river’s morphological state and physicochemical conditions. Moreover, consequent changes in the structure and functioning of the aquatic community have a tendency to negatively affect various ecosystem services, thereby putting local societies at risk and undermining the goal of sustainable development. Various qualitative global assessments have certainly helped illustrating opportunities and threats, but have failed to be compatible with local management needs and ecological perspectives. Therefore, the aim of this research is to monitor, analyse, evaluate and illustrate the impacts of reservoir-based hydropower infrastructure on the morphology, hydrology and quality of Andean headwaters within the Amazon river basin by combining (i) remote sensing, (ii) process-based hydrological modelling and (iii) water quality assessment based on field campaigns with a high temporal resolution. Additional focus is directed at the interaction with climate change, including the contribution through emissions of greenhouse gases (field measurements) and the challenges under future climate conditions (modelling). To do so, the Paute river basin (Ecuador) is selected as study area to (i) overcome the local data scarcity, (ii) develop a protocol for evaluating similar systems and (iii) preserve the uniqueness of these headwater ecosystems. Project activities and obtained results will be publicly accessible and continuously disseminated online and in-person. As such, this research will increase local and global understanding of and reduce the environmental impacts associated with reservoir-based hydropower installations.