Freeze/thaw (F/T) processes can be quite different under the various land surface types found in the heterogeneous polygonal tundra of the Arctic. Proper simulation of these different processes is essential for accurate prediction of the release of greenhouse gases under a warming climate scenario. In this study we have modified the dynamic organic soil version of the Terrestrial Ecosystem Model (DOS-TEM) to simulate F/T processes beneath the polygon rims, polygon centers (with and without water), and lakes that are common features in Arctic lowland regions. We first verified the F/T algorithm in the DOS-TEM against analytical solutions, and then compared the results with in situ measurements from Samoylov Island, Siberia. In the final stage, we examined the different responses of the F/T processes for different water levels at the various land surface types. The simulations revealed that (1) the DOS-TEM was very efficient and its results compared very well with analytical solutions for idealized cases, (2) the simulations compared reasonably well with in situ measurements although there were a number of model limitations and uncertainties, (3) the DOS-TEM was able to successfully simulate the differences in F/T dynamics under different land surface types, and (4) permafrost beneath water bodies was found to respond highly sensitive to changes in water depths between 1 and 2 m. Our results indicate that water is very important in the thermal processes simulated by the DOS-TEM; the heterogeneous nature of the landscape and different water depths therefore need to be taken into account when simulating methane emission responses to a warming climate.