This dataset presents the assessment of the lake types and settings together with the data on hydrophysical parameters measurements including Electrical Conductivity, on-site water temperature and pH, except at one lake (EN21426-2) of which electrical conductivity was measured in the Hydrochemical Laboratory of AWI). Lakes were surveyed between 6 August and 2 September 2021. A total of 66 lakes in Central and Eastern Yakutia were assessed as part of the joint Russian-German expedition (NEFU-AWI; RU-Land_2021_Yakutia). Of those 66 lakes, 15 are from mountain lakes located within the Verkhoyansk mountain range, at the eastern end of the expedition route, including mostly intermontane basin or glacial lakes (average elevation: c. 1080 m a.s.l.). 13 lakes were sampled in Oymyakonsky District and two lakes in Tomponsky District. The hydrochemical dataset from the other 52 lakes that lie within the eastern extent of the Central Yakutian Lowland (average elevation: c. 190 m a.s.l.) represents thermokarst lakes. Thermokarst lakes originate from thawing of ice-rich permafrost and were found in different stages of their development, with a wide range of anthropogenic impact. These 52 thermokarst lakes include seven lakes within the Churapchinsky District, two are located in the Tattinsky District further east within a freshly burned forest. 42 lakes are located in Megino-Kangalassky District, of which 17 lakes are around Tungulu, and 24 lakes around Maya settlements.