The thermal use of the underground for heating and cooling applications can be done with borehole heat exchangers. This work deals with the further development of the modelling of thermal transport processes inside and outside the borehole as well as with the application of the further developed models. The combination of high accuracy and short computation time is achieved by the development of three-dimensional thermal resistance and capacity models for borehole heat exchangers. Short transient transport processes can be calculated by the developed model with a considerable higher dynamic and accuracy than with known models from literature. The model is used to evaluate measurement data of a thermal response test by parameter estimation technique with a transient three-dimensional model for the first time. Clear advantages like shortening of the test duration are shown. The developed borehole heat exchanger model is combined with a three-dimensional description of the underground in the Finite-Element-Program FEFLOW. The influence of moving groundwater on borehole heat exchangers and borehole thermal energy stores is then quantified.