Understanding disaster risk is the first priority for action of the Sendai Framework for Disaster Risk Reduction (SFDRR) and is the essential information needed to guide disaster governance and achieve disaster risk reduction. Flooding is a natural hazard which causes the highest number of affected people due to disasters. In Ecuador from 1970 to 2019 flooding caused the highest amount of loss and damage to housing, and from 2016 to 2019 there were 1263 flood events reported. However, the differentiated impacts in flood exposed areas and what can be done to reduce risk and its impacts, it is still not well understood. In this research, we explored the different dimensions of flood risk, namely hazard, exposure, and vulnerability, and investigated the drivers of risk in different ecological regions of Ecuador. The assessment was conducted at the parish level, the smallest administrative scale, for three selected provinces of Bolivar, Los Ríos and Napo, representing not only the country’s three main ecological regions but also commonly affected territories due to flooding. Using automated flood detection procedure based on Sentinel-1 synthetic aperture radar data, flood hazard information was derived from flood frequency and flood depth for the years 2017, 2018 and 2019. The drivers of exposure and vulnerability were derived from scientific literature and further evaluated and complemented during a participatory workshop with over 50 local experts from the different regions. Centered on this exercise, an indicator library was created to inform the data selection from various sources and provides the basis for deriving a spatially explicit flood risk assessment using an indicator-based approach. Impact data are available to validate the risk assessment at the parish level and with this reveal key drivers of flood risk in different ecological regions of Ecuador. This information will provide the basis to derive targeted measures for disaster risk reduction.