AbstractWater volume estimates of shallow desert lakes are the basis for water balance calculations, important both for water resource management and paleohydrology/climatology. Water volumes are typically inferred from bathymetry mapping; however, being shallow, ephemeral, and remote, bathymetric surveys are scarce in such lakes. We propose a new, remote‐sensing‐based, method to derive the bathymetry of such lakes using the relation between water occurrence, during >30 year of optical satellite data, and accurate elevation measurements from the new Ice, Cloud, and Land Elevation Satellite‐2 (ICESat‐2). We demonstrate our method at three locations where we map bathymetries with ~0.3 m error. This method complements other remotely sensed, bathymetry‐mapping methods as it can be applied to: (a) complex lake systems with subbasins, (b) remote lakes with no in‐situ records, and (c) flooded lakes. The proposed method can be easily implemented in other shallow lakes as it builds on publically accessible global data sets.