The assessment of flood disasters is considered an essential factor in land use management, being necessary to understand and define the magnitude of past events. In this regard, several flood diagnoses have been developed using Sentinel-2 multispectral imagery, especially in large water bodies. However, one of the main challenges is still related to floods, where water surfaces have sizes similar to the spatial resolution of the analyzed satellite images, being difficult to detect and map. Therefore, the present study developed a combined methodology for flood mapping in small-sized water bodies using Sentinel-2 MSI imagery. The method consisted of evaluating the effectiveness of the application and combination of (a) a super-resolution algorithm to improve image resolution, (b) a set of seven spectral indices for highlighting water-covered areas, such as AWE indices, and (c) two methods for flood mapping, including a machine learning method based on unsupervised classification (EM cluster) and 14 thresholding methods for automatic determination. The processes were evaluated in the Carrión River, Palencia, Spain. It was determined that the approach with the best results in flood mapping was the one that combined AWE spectral indices with methods such as Huang and Wang, Li and Tam, Otsu, moment preservation, and EM cluster classification, showing global accuracy and Kappa coefficient values higher than 0.88 and 0.75, respectively, when applying the quantitative accuracy index.