Georeferencing accuracy plays a crucial role in providing high-quality ready-to-use remote sensing data. The georeferencing of nighttime thermal satellite imagery conducted by matching to a basemap is challenging due to the complexity of thermal radiation patterns in the diurnal cycle and the coarse resolution of thermal sensors in comparison to sensors used for imaging in the visual spectral range (which is typically used for creating basemaps). The presented paper introduces a novel approach for the improvement of the georeferencing of nighttime thermal ECOSTRESS imagery: an up-to-date reference is created for each to-be-georeferenced image, derived from land cover classification products. In the proposed method, edges of water bodies are used as matching objects, since water bodies exhibit a relatively high contrast with adjacent areas in nighttime thermal infrared imagery. The method was tested on imagery of the East African Rift and validated using manually set ground control check points. The results show that the proposed method improves the existing georeferencing of the tested ECOSTRESS images by 12.0 pixels on average. The strongest source of uncertainty for the proposed method is the accuracy of cloud masks because cloud edges can be mistaken for water body edges and included in fitting transformation parameters. The georeferencing improvement method is based on the physical properties of radiation for land masses and water bodies, which makes it potentially globally applicable, and is feasible to use with nighttime thermal infrared data from different sensors.