In karst aquifers, temperature distribution play an additional important role since they carry information about internal aquifer structures. The aim of the present work is to develop a two dimensional heat transfer model in a karst aquifer. Navier Stokes equation is used to simulate the groundwater velocity in the conduit system where the porosity tends to one, and means water velocity was taken into account in the fractured rock. Heat transport equation was applied to simulate the temperature distribution in a karst aquifer, and k- turbulent model is used to simulate the turbulent viscosity. The model was applied to the karst system of Val d'Orléans. Temperatures are measured in thirteen wells with different depth in 29 Jun 2011. Results have shown that the model was not sensitive to the variation of water density, but it is sensitive to the variation of specific heat and density of the rock especially in the fractured system. Also, the model was varied sharply with the velocity of water in sinkhole points, and any variation in the depth of saturated zone. The comparison between measured and calculated temperatures in wells is very good.