A three-dimensional computational tool was developed that simulates the heat and mass transfer interaction in a soil-root-stem system (SRSS) for a tree in a seasonally varying deciduous forest. The development of the SRSS model involved the modification and coupling of existing heat and mass transport tools to reproduce the three-dimensional diurnal internal and external temperatures, internal fluid distribution, and heat flow in the soil, roots, and stems. The model also required the development of a parallel Monte-Carlo algorithm to simulate the solar and environmental radiation regime consisting of sky and forest radiative effects surrounding the tree. The SRSS was tested, component-wise verified, and quantitatively compared with published observations. The SRSS was applied to simulate a tree in a dense temperate hardwood forest that included the calculations of surface heat flux and comparisons between cases with fluid flow transport and periods of zero flow. Results from the winter simulations indicate that the primary influence of temperature in the trunk is solar radiation and radiative energy from the soil and surrounding trees. Results from the summer simulation differed with previous results, indicating that sap flow in the trunk altered the internal temperature change with secondary effects attributed to the radiative energy from the soil and surrounding trees. Summer simulation results also showed that with sap flow, as the soil around the roots become unsaturated, the flow path for the roots will be changed to areas where the soil is still saturated with a corresponding increase in fluid velocity.