This dataset presents measurements of stable isotopes in water (δD and δ18O) from Lake Locknesjön, Sweden. Water samples were collected between 2013 and 2018 and were taken from different depths down to 20 m in the lake, as well as from the lake's main tributary and its outflow. Depending on the depth, the water samples were collected from the shore, by a diving team, or with a UWITEC gravity corer. Measurements of stable isotopes in water samples were conducted at the Laboratoire des Sciences du Climat et de l'Environnement (LSCE), Gif-sur-Yvette, France. The δ18O was measured with a Finnigan MAT252 isotope ratio mass spectrometer with a precision of ±0.05‰ (two standard deviations). The δD was measured with a Picarro Analyzer (Cavity Ring-Down Spectroscopy) with a precision of±0.7‰ (one standard deviation).