This data set includes the 50 m and 200 m bathymetry model for the Lena Delta region covering 232,700 km2 stretching from Cape Mamontov Klyk in the western Laptev Sea to Kotelny Island in the New Siberian Islands. The models were calculated with the topo to raster tool in ArcGIS TM version 10.6 based on depth points and isobaths lines derived from large-scale current and historical nautical maps.The final bathymetry models are available in GeoTiff format in 50 m (TTR_50m_LenaDelta.tif) and 200 m (TTR_200m_LenaDelta.tif) spatial resolution. In addition, the data set includes the complete input data for the bathymetry models. The input data consists of a point shapefile (Depth_points_LenaDelta.shp) including 50,828 manually digitized depth point measurements, a polyline shapefile (Isobaths_LenaDelta.shp) including 720 manually digitized isobath lines and a polygon shapefile (Water_area_LenaDelta.shp) for the water extent.The Lena Delta region bathymetry was validated with depth data derived from ship cruises in 2019 (Fuchs et al. submitted, Palmtag et al., 2021) as well as water depth data available on PANGAEA (e.g. Hölemann et al., 2020).