Thermokarst lakes are typical features of the northern permafrost ecosystems which highly affect the thermal exchange between the atmosphere and the subsurface. The objective of this work is to describe the physiographic character and the crucial thermal processes of the lakes and to explore possibilities and limitations of the application of FLake to these specific water bodies. The particular lake modeled within this study is located in the Lena river delta (Siberia) and embedded in the predominant lake-rich permafrost landscape which is significantly influenced by thermokarst processes. Meteorological and lake temperature data spanning several years were used for model setup and validation. The resulting model parameters were analyzed by Monte Carlo simulations. The winter thermal regime is characterized by an ice cover up to 2 m thick that lasts for about 7 months per year. Lake bottom temperatures increase at the start of the ice-covered period due to upward-directed heat flux from the sediment at a rate of less than 1 W m-2. Ice breaks up in June with maximum downward fluxes over the summer months of about 5 W m-2. Complete mixing occurs within the entire water column from the start of ice break-up and continues during the ice-free periods, while stratification just occurs sporadic. Agreement between the FLake model output and lake temperature measurements is good during the ice-free months in summer while there are larger deviations during the ice-covered period. This might be explained with the effects of solar radiation penetrating through the ice and leading to a heating of the water below which is not represented in FLake.