This data set includes the CTD cast locations, which were measured during the CACOON 2019 expeditions (Fuchs et al., 2021; Strauss et al., 2021) in the Lena Delta region in Siberia.The data collection took place during two field campaigns; the first one was in March-April 2019, the second one in August 2019. Measurements were taken with a handheld SontekTM CastAway sensor with an integrated GPS. The measured data include pressure, depth, temperature, conductivity, specific conductance, salinity, sound velocity, and density. In total, 31 depth profiles were measured from the Sardakhskaya main river channel in the Lena Delta to 80 km offshore in the Laptev Sea to specifically target the mouth area of the Sardakhskaya channel. The CTD was lowered from water surface with an additional ballast to make sure the small CTD device reached the sea (or river) bed.This data sets includes detailed data about the locations, time and duration of CTD measurements in the Lena Delta region.