Geothermal or ground source heat pumps (GSHPs) are among the growing renewable energy technologies used for heating and cooling of buildings. However, little work has been done to investigate their geo-environmental effects within the subsurface, especially in contaminated environments. This research uses FEFLOW software, to simulate heat and mass transport of a vertical closed-loop GSHP system. Transient flow and heat transport results for a multiple borehole system are presented for a hypothetical building located in Toronto, Canada, and shows long-term effects on subsurface temperature. Moreover, the impact of heat exchanged with the subsurface on biodegradation kinetics is examined in a contaminant transport simulation, to evaluate the possibility of utilizing this heat as a remediation strategy. The results revealed that temperature changes caused by GSHP operation can significantly enhance biodegradation of hydrocarbon contaminants. For instance, elevated subsurface temperature resulted in 96% reduction in benzene concentration, after one year of GSHP simulated operation for an office building located in Toronto, Canada.