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 the freshwater lake model FLake to these specific water bodies. The particular lake modeled within this study is located on Samoylov island in the Lena river delta (Siberia) and embedded in the predominant lake-rich permafrost landscape, which is significantly influenced by thermokarst processes. Meteorological data are used to model lake temperature dynamics. This contains radiation (incoming short and long wave), air temperature, vapor pressure of water and wind speed from a nearby meteorological station build up in 2002. Directly measured lake temperatures in different depths are used for validation. All variables are cropped to the same period (July 2009 to August 2011) and interpolated to hourly values. The model FLake from IGB calculated water temperatures from meteorological data, based on parameters from an educated guess. Following, some of these parameters are varied via Monte Carlo simulation and resulting measured of fit are analysed. Agreement between the FLake model output and lake temperature measurements is generally good. Best Monte Carlo runs show a RMSE below 1 K and R2 above 0.9 during the ice-free months in summer while larger deviations occur 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. To access the specific characteristics of the model a Monte Carlo simulation was set up. It shows a clear interdependence between the extinction coefficient and the lake depth. To avoid possible problems of FLake according shallow and ice-rich lakes, this setup was split into ice-free and ice-full seasons.