Due to the similarity of the radar backscatter over open water and over sand surfaces a reliable near real-time flood mapping based on satellite radar sensors is usually not possible in arid areas. Within this study, an approach is presented to enhance the results of an automatic Sentinel-1 flood processing chain by removing overestimations of the water extent related to low-backscattering sand surfaces using a Sand Exclusion Layer (SEL) derived from time-series statistics of Sentinel-1 data sets. The methodology was tested and validated on a flood event in May 2016 at Webi Shabelle River, Somalia and Ethiopia, which has been covered by a time-series of 202 Sentinel-1 scenes within the period June 2014 to May 2017. The approach proved capable of significantly improving the classification accuracy of the Sentinel-1 flood service within this study site. The Overall Accuracy increased by ~5% to a value of 98.5% and the User’s Accuracy increased by 25.2% to a value of 96.0%. Experimental results have shown that the classification accuracy is influenced by several parameters such as the lengths of the time-series used for generating the SEL.