This data set provides lake bathymetry data for three lakes situated in a large thermokarst basin (alas) in the ice-rich permafrost deposits (Yedoma-type Ice Complex) of Kurungnakh Island, Lena Delta. It consists of three point shapefiles, one for each lake. In addition to the lake bathymetry points, the shapefiles contain shoreline points that delineate the lakes' boundaries.Bathymetry was measured along several profiles in August 2008 using a Garmin GPSmap 178c sounder and a handheld echo sounder on board a small non-motorized rubber boat. Shoreline points were measured using a ZEISS ELTA C30 tacheometer with an electro‐optical distance measurement device and were set to a lake depth of zero. The measurement method for each point is given in the attribute tables of the shapefile.