The article presents the geomorphological and geochemical investigation of the water bodies on the Samoylov and Kurunghnakh Islands, the Lena River delta. We used GIS-analyze analysis for identifying water body groups, depending on their geomorphological features. The studied water bodies are located on two principally different surfaces: the first and the third terraces of the Lena Delta. The water bodies occupy thermokarst hollow bottoms, which have various elevations above sea level. We identified the altitudes of the water bodies water surfaces by analysing with ArcticDEM. Additionally, we estimated the area of the water bodies by hand after mapping the borders of the water bodies in UAV imageries. We sampled the bottom sediments and water's chemical composition. All water bodies were divided into groups: (1) small water bodies on the Yedoma upland surface; (2) water bodies in six thermokarst hollows; (3) water bodies on the first terrace. The water bodies bottom sediments on the Yedoma are depleted by the As and enriched by the Zn and Mo in comparison with sediments of other groups. The Rare Earth Elements concentrations in the bottom sediments of Yedoma water bodies and several water bodies on poorly degraded surfaces of the third terrace are lower than in other water bodies, except La.