Shallow geothermal energy is increasingly adopted for heating and cooling purposes because of the short pay-back time of initial installation investments. As a result, a relevant concentration of Ground Heat Exchangers is being experienced in urban areas. Planning issues thus arise to manage interferences and optimize the use of underground heat resources without depletion, harm to the environment nor efficiency losses on heat pumps or plant oversizing. This study provides a rational approach to optimise geothermal resources based on the use of Geographic Information Systems and transient 3D Thermo-Hydro numerical models. An optimised semi-analytical formula for the assessment of Borehole Heat Exchangers geothermal potential in hydrodynamic conditions is developed through a parametric numerical study. The long-term performances of BHE subjected to groundwater velocity in the range of 0 to 1 m/day were analysed with multiple aquifer thermal parameters. This analytical expression allows a fast and accurate assessment of the potential even in large areas without leading to excessively conservative evaluations. This may serve designers in the preliminary sizing of installations and city planners in the development of appropriate policies for the promotion and management of shallow geothermal resources. An example of the application to the central district of the city of Turin (Italy) is also shown.