Water 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-yr 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 sub-basins, (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.