This dataset contains CTD measurements, taken together with temperature gradient or gas concentration measurements in September 2021 at 53 locations off Tuktoyaktuk Island and in a small lake (“Lake 3”) between the villages of Tuktoyaktuk and Inuvik, as well as in a former river channel (“Swiss Cheese Lake”) in the Mackenzie Delta, Northwest Territories, Canada. The measurements were part of the “Mackenzie Delta Permafrost Field Campaign” (mCan2021) within the “Modular Observation solutions for Earth Systems” (MOSES) program. Data is recorded using a CastAway-CTD that is manually lowered to the bottom of the lake or ocean at the measurement sites and contains information about water conductivity, temperature and depth and GPS position. Especially the water temperature and conductivity/salinity are important for gas concentration data processing. The data are provided as unprocessed raw data.