Bathymetry from small lakes in the Arctic is generally not available; however, this type of data is useful in interpreting other data, such as geoelectric surveys. To this end, we deployed a small automated boat carrying a sonar sensor to measure water depth and a GNSS to measure position on two lakes: Swiss Cheese Lake” (69.2320°N / 135.2513°W) between Sept. 13 and 16, 2021 and at “Lake 3” (68.7763°N / 133.5404°W) on Sept. 18, 2021. The boat is approximately 80 cm long and propelled with a single thruster. The boat uses a Pixhawk 4 controller to automate it's movement and record all the data from the mission. An Airmar SS510 transducer measures water depth (bathymetry) at 200kHz, with beam width of 9°, and can measure from 0.4 to 200m with a resolution of 1cm (depth accuracy 99.46% at full range). The boat has two GNSS (GPS) receivers; one U-blox Neo-M8N (2.5m position accuracy) and one Emlid Reach M+. The Reach M+ is capable of cm level positioning when used with a base station (RTK) or if the data are post processed (PPK) after data collection. Available here are both the raw and processed datasets in different formats. Please see the included Readme_mcan21_BathyBoat.pdf for detailed information on the datafiles and data processing.