This data set includes the 50 m and 200 m bathymetry model for the Kolyma Gulf region covering an area of 12,100 km2 extending from the apex of the Kolyma Delta (5 km downstream of the city of Cherskiy) to 70 km offshore into the East Siberian Sea. 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. In addition, the water area extent for this region was derived from the Global Surface Water layer by Pekel et al. (2016).The final bathymetry models are available in GeoTiff format in 50 m (TTR_50m_KolymaGulf.tif) and 200 m (TTR_200m_KolymaGulf.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_KolymaGulf.shp) including 24,126 manually digitized point depth measurements, a polyline shapefile (Isobaths_KolymaGulf.shp) including 1,053 manually digitized isobath lines and a polygon shapefile (Water_area_KolymaGulf.shp) for the water extent.The Kolyma Gulf region bathymetry was validated with depth data derived from ship cruises in 2019 (Palmtag and Mann, 2021).