Flood mapping and water depth estimation from Synthetic Aperture Radar (SAR) imagery are crucial for calibrating and validating hydraulic models. This study uses SAR imagery to evaluate various preprocessing (especially speckle noise reduction), flood mapping, and water depth estimation methods. The impact of the choice of method at different steps and its hyperparameters is studied by considering an ensemble of preprocessed images, flood maps, and water depth fields. The evaluation is conducted for two flood events on the Garonne River (France) in 2019 and 2021, using hydrodynamic simulations and in-situ observations as reference data. Results show that the choice of speckle filter alters flood extent estimations with variations of several square kilometers. Furthermore, the selection and tuning of flood mapping methods also affect performance. While supervised methods outperformed unsupervised ones, tuned unsupervised approaches (such as local thresholding or change detection) can achieve comparable results. The compounded uncertainty from preprocessing and flood mapping steps also introduces high variability in the water depth field estimates. This study highlights the importance of considering the entire processing pipeline, encompassing preprocessing, flood mapping, and water depth estimation methods and their associated hyperparameters. Rather than relying on a single configuration, adopting an ensemble approach and accounting for methodological uncertainty should be privileged. For flood mapping, the method choice has the most influence. For water depth estimation, the most influential processing step was the flood map input resulting from the flood mapping step and the hyperparameters of the methods.