The thermal regime in the sediment column below shallow bodies of water in Arctic permafrost controls benthic habitats and permafrost stability. We present a robust, portable device that measures detailed temperature–depth profiles of the near-surface sediments in less than 1 h. Test campaigns in the Canadian Arctic and on Svalbard have demonstrated its utility in a range of environments during winter and summer. Measured temperatures were spatially heterogeneous, even within single bodies of water. We observed the broadest temperature range in water less than 1 m deep, a zone that is not captured by single measurements in deeper water.