S.M.alfieri-1@tudelft.nl (S.M.A.); M.Menenti@tudelft.nl (M.M.)Abstract: Small reservoirs play an important role in mining, industries, and agriculture, but storage levels or stage changes are very dynamic. Accurate and up-to-date maps of surface water storage and distribution are invaluable for informing decisions relating to water security, flood monitoring, and water resources management. Satellite remote sensing is an effective way of monitoring the dynamics of surface waterbodies over large areas. The European Space Agency (ESA) has recently launched constellations of Sentinel-1 (S1) and Sentinel-2 (S2) satellites carrying C-band synthetic aperture radar (SAR) and a multispectral imaging radiometer, respectively. The constellations improve global coverage of remotely sensed imagery and enable the development of near real-time operational products. This unprecedented data availability leads to an urgent need for the application of fully automatic, feasible, and accurate retrieval methods for mapping and monitoring waterbodies. The mapping of waterbodies can take advantage of the synthesis of SAR and multispectral remote sensing data in order to increase classification accuracy. This study compares automatic thresholding to machine learning, when applied to delineate waterbodies with diverse spectral and spatial characteristics. Automatic thresholding was applied to near-concurrent normalized difference water index (NDWI) (generated from S2 optical imagery) and VH backscatter features (generated from S1 SAR data). Machine learning was applied to a comprehensive set of features derived from S1 and S2 data. During our field surveys, we observed that the waterbodies visited had different sizes and varying levels of turbidity, sedimentation, and eutrophication. Five machine learning algorithms (MLAs), namely decision tree (DT), k-nearest neighbour (k-NN), random forest (RF), and two implementations of the support vector machine (SVM) were considered. Several experiments were carried out to better understand the complexities involved in mapping spectrally and spatially complex waterbodies. It was found that the combination of multispectral indices with SAR data is highly beneficial for classifying complex waterbodies and that the proposed thresholding approach classified waterbodies with an overall classification accuracy of 89.3%. However, the varying concentrations of suspended sediments (turbidity), dissolved particles, and aquatic plants negatively affected the classification accuracies of the proposed method, whereas the MLAs (SVM in particular) were less sensitive to such variations. The main disadvantage of using MLAs for operational waterbody mapping is the requirement for suitable training samples, representing both water and non-water land covers. The dynamic nature of reservoirs (many reservoirs are depleted at least once a year) makes the re-use of training data unfeasible. The study found that aggregating (combining) the thresholding results of two SAR and multispectral features, namely the S1 VH polari...