Shallow geothermal systems (SGSs) for building climatization represent an advantageous alternative to traditional air-conditioning systems, resulting in economic and environmental benefits. Installation of these systems requires knowledge of site-specific geological and hydrogeological conditions, which in feasibility studies are often evaluated only at the single plant scale, lacking a comprehensive view and risking not to guarantee the system sustainability over time. In this paper a methodology for the sustainable design of SGSs is presented. The methodology is developed from an example on the aquifer scale in Longarone (Belluno, Italy), where three groundwater heat pumps (GWHPs) were installed in an industrial area located in a mountain basin hosting a coarse-grained phreatic aquifer, characterized by sediments with high hydraulic conductivity and proximal to a large river (Piave River). Open-loop systems were first analyzed through numerical modeling using FEFLOW software, identifying peculiar features of the aquifer, due to its interaction with surface waters, and suggesting the possibility of its greater geothermal exploitation. Subsequently, a relationship between flow rates and thermal plume extensions was obtained, which is useful to providing support in the evaluation of potential interference with neighboring systems. The study at the aquifer scale proved representative of the system, highlighting the criticalities of the area, such as trends of aquifer temperature alteration, interference between plants, and thermal feedback.