Lakes and ponds are abundant in vast regions of the permafrost lowland landscapes in the Arctic. The areal fraction of open water surfaces can amount to more than 25 % in some lowland tundra landscapes. In some tundra landscapes, about 50 % of the total number of water bodies feature surface areas less than 10 m2. Several studies emphasize that these water bodies strongly control fundamental ecosystem processes such as the carbon, heat, and water balance. So far, it is poorly understood how these ecosystems will respond to changing climate conditions. In particular, the presence of water bodies is strongly related to the stability of the surrounding permafrost soils. Permafrost is an effective water barrier that largely controls lake formation, drainage, and growth. In return, water bodies strongly affect the thermal state of the surrounding permafrost by modifying the surface energy balance and the subsurface heat transport and storage capabilities. In order to gain a better understanding of the vulnerability of such landscapes the 1D transient permafrost model CryoGrid3 was coupled to the 1D lake model FLake. The development of the model was supported by a large observational dataset of water temperature profile measurements from lakes and ponds in northern Siberia. The coupled model was used for site level simulations for water bodies on Samoylov Island located in the Lena River Delta. Based on extensive Monte-Carlo sensitivity tests, we investigated the thermal impact of water bodies with different depths (0.2 – 5.0 m) on the thermal state of sediments underneath. Climate impact simulations until 2100 were performed considering a moderate and a strong climate warming scenario. The preliminary results suggest that shallow water bodies (water depth < 1.5 m) can accelerate permafrost thaw by a factor of five. More importantly, the difference in permafrost thaw rate between moderate and strong climate warming vanish for water bodies deeper than 0.8 m. Furthermore, the results demonstrate that lateral heat fluxes play an important role for stabilizing permafrost underneath small water bodies.