Remote sensing data are essential for monitoring Earth’s surface waters, especially since the number of publicly available in-situ data is declining. Satellite altimetry provides valuable information on water level and its variations for lakes, reservoirs, and rivers. In combination with satellite imagery, the derived time series allow for monitoring lake storage changes and river discharge. However, satellite altimetry is limited in spatial resolution due to its measurement geometry, only providing information in nadir direction beneath the satellite’s orbit. In a case study in the Mississippi River Basin (MRB), this study investigates the potential and the limitations of past and current satellite missions to monitor basin-wide storage changes. For that purpose an automated target detection is developed and the extracted lake surfaces are merged with the satellites’ tracks. This reveals that the current altimeter configuration misses about 80% of all lakes larger than 0.1 km2 in the MRB, and still 20% of lakes larger than 10 km2, corresponding to 30% and 7% of surface area, respectively. Past altimetry configurations perform even worse. From the water bodies represented by a global hydrology model, at least 91% of targets and 98% of storage changes are captured by the current altimeter configuration. This will significantly improve with the launch of the planned SWOT mission.