Ground source heat pump systems are widely available as energy-saving systems for heating/cooling buildings, hot water supply, snow melting and other heat uses through heat exchanges between borehole heat exchangers and the underground of stable temperature. It has been long discussed that the size of borehole heat exchanger should be optimized in each condition of geology and hydrogeology. An advection effect in heat transfer by groundwater flow contributes to size reduction of borehole heat exchangers, when the groundwater flows with relatively high velocity, for example over several tens meters per year of Darcy velocity. This paper proposes a determination methodology of an optimized size for a ground heat exchanger considering groundwater flow in main watersheds basins for living in Japan. This study developed previous models of groundwater flow simulation in terms of high-resolution grid and hydraulic conductivity Furthermore, operation simulation of ground heat pump systems was performed to determine an optimal length of a borehole heat exchanger in two necessary temperature conditions and one performance condition. As a result, the oval average of calculated optimal lengths was 77.5m, and individual average in each basin increased in the northern direction depending on the heating loads. The size reduction by groundwater flow was 3.4m in average, and the reduction increased 9.1m when Darcy flow velocity was high (>20m/y). The negative correlation between Darcy flow velocities and optimal sizes was obvious and the correlation increased when the heating loads increased or when the ground thermal conductivities were small.