A two-dimensional transient model has been developed using COMSOL Multiphysics modeling software to simulate the heat transfer processes from a row of heated pipes in horizontally layered media consists of two porous sublayers with different permeabilities. The application of the present study is related to thermal energy storage or radiant floor heating system using the embedded piping system as the heat source. The present numerical simulation was first compared and validated using a parallel experimental work. The transient temperature profiles of the layered system obtained from both the experimental and numerical work are in good agreement. Once the numerical code is validated, a parametric numerical study has been performed to investigate the effects of layered system configurations on the heat transfer characteristics. Porous media with different properties were modeled using the subsurface flow (Brinkman’s model formulation) and heat transfer module. Different layered system configurations were simulated by adjusting the sublayer thicknesses and using different permeability ratios for the layered system. For a layered porous system with different permeabilities, the dominant mode of heat transfer changes from heat conduction to heat convection depending on the ratio of the porous layer permeabilities. The interface location of the two media relative to the depth of the embedded heated pipes also plays an important role in the heat transfer results. The numerical results are presented in contour plots to examine the temperature distribution within the layered system (for energy storage application) as well as along the top surface of the system (for radiant floor heating application). The heat transfer results suggest that the layer configuration of the media plays an important role in the performance of radiant floor heating system.