Regions of warm, thin, discontinuous permafrost have been observed to be experiencing rapid changes in lake and pond dynamics in recent decades. Even though surface water and groundwater interactions are thought to play a significant role in heat transport in these regions, the effect of these interactions on permafrost remains largely unquantified. In order to examine the influence of groundwater flow on permafrost dynamics, we modeled the development of a sub-lake talik under permafrost conditions similar to those observed in the southern-central Seward Peninsula region of Alaska using a numerical solution that couples heat transport and groundwater flow, including the effect of water phase changes on soil permeability and latent heat content. A comparison of model simulations, with and without near surface subpermafrost groundwater flow, indicates that stable permafrost thicknesses are 2 to 5 times greater in the absence of groundwater flow. Simulations examining the thermal influence of lakes on underlying permafrost suggest that a through-going talik can develop in a matter of decades and that the incorporation of advective heat transport reduces the time to complete loss of ice beneath the lake by half, relative to heat transport by conduction alone. This work presents the first quantitative assessment of the rates of sub-lake permafrost response to thermal disturbances, such as talik development, in systems with near-surface groundwater flow. The results highlight the importance of coupled thermal and hydrologic processes on discontinuous permafrost dynamics.