This data set includes spatial high-resolution bathymetry data sets for the Lena Delta and Kolyma Gulf regions. Based on large-scale current and historical nautical maps, depth points and isobaths lines were manually digitized and served as input data for the bathymetry models. The models were calculated with the topo to raster tool in ArcGIS TM version 10.6 into a 50 m (TTR50) and a 200 m (TTR200) grid cell bathymetry for both regions. The models were validated with depth data derived from ship cruises in 2019 (Fuchs et al., submitted, Palmtag et al., 2021, Palmtag and Mann, 2021) and water depth data available on PANGAEA (e.g. Hölemann et al., 2020).Beside the bathymetry models for the Lena Delta and Kolyma Gulf regions which are available in GeoTiff format, this data set contains the complete input data for the models, which includes the depth point data, the isobaths lines, and the water area extent in shapefile format for both regions.