River discharge is an Essential Climate Variable important for many climate and socio-economical applications. The relative paucity of in situ river discharge data makes the development of satellite-based methods for discharge estimation attractive. The main approaches rely on a combination of satellite altimetry, providing the measurements of river water level, and optical satellite sensors, allowing the estimation of river width, and on conversion of these parameters to the discharge. The present paper explores the potential of Sentinel-3A & B and Sentinel-6 SAR altimetry missions for discharge estimation using the Rhine and Po Rivers as a case study. We explore the effect of different approaches of discharge estimation and altimetry data treatment on the accuracy of the obtained discharge. We show that enhanced high-resolution 80 Hz processing of SAR altimetry signal as well as rigorous satellite data selection and filtering protocols, are both beneficial for the accuracy of the water level and the resulting discharge retrieval. Depending on the water level product, an accuracy of 4–16%, expressed as Normalised Root Mean Square Error (NRMSE), is achieved with an empirical rating curve, constructed between each water level dataset and simultaneous in situ discharge measurements. With a physical method, based on the Manning equation, an accuracy of 11–26% NRMSE is attained. The latter improves to 8–22% after introducing the variable channel roughness term into the Manning equation. We also demonstrate that for the medium-size Rhine and Po Rivers the errors of 10% (NRMSE) can be potentially achieved with a semi-empirical approach of the discharge estimation based on simplified physical laws (called here Bjerklie equation) after regional adjustment of both conductance and exponential parameters of the equation. We conclude that if similar accuracy will be attained in future for other medium-sized European rivers, such high-quality SAR altimetry-based ECV discharge products would be able to detect the 4–15% of discharge change, which is projected to 2080 in Europe in the intermediate IPCC Shared Socio-economic Pathway scenario SSP2-4.5.