Spaceborne Synthetic Aperture Radar (SAR) are well-established systems for flood mapping, thanks to their high sensitivity towards water surfaces and their independence from daylight and cloud cover. Particularly able is the 2014-launched Copernicus Sentinel-1 C-band SAR mission, with its systematic monitoring schedule featuring global land coverage in a short revisit time and a 20 m ground resolution. Yet, variable environment conditions, low-contrasting land cover, and complex terrain pose major challenges to fully automated flood monitoring. To overcome these issues, and aiming for a robust classification, we formulate a datacube-based flood mapping algorithm that exploits the Sentinel-1 orbit repetition and a priori generated probability parameters for flood and non-flood conditions. A globally applicable flood signature is obtained from manually collected wind- and frost-free images. Through harmonic analysis of each pixel’s full time series, we derive a local seasonal non-flood signal comprising the expected backscatter values for each day-of-year. From those predefined probability distributions, we classify incoming Sentinel-1 images by simple Bayes inference, which is computationally slim and hence suitable for near-real-time operations, and also yields uncertainty values. The datacube-based masking of no-sensitivity resulting from impeding land cover and ill-posed SAR configuration enhances the classification robustness. We employed the algorithm on a 6-year Sentinel-1 datacube over Greece, where a major flood hit the region of Thessaly in 2018. In-depth analysis of model parameters and sensitivity, and the evaluation against microwave and optical reference flood maps, suggest excellent flood mapping skill, and very satisfying classification metrics with about 96% overall accuracy and only few false positives. The presented algorithm is part of the ensemble flood mapping product of the Global Flood Monitoring (GFM) component of the Copernicus Emergency Management Service (CEMS).