This paper presents a retrospective analysis of two projects undertaken by the Services Industriels de Genève, focusing on the sustainable use of shallow Quaternary aquifers (<60m depth) in Geneva, Switzerland, for geothermal heating and cooling. Given the relatively slow groundwater flow velocities of these aquifers, the development, in collaboration with the State of Geneva through the Geothermies program, of hydrogeological models for long-term temperature variations prediction of these aquifers is essential for ensuring their sustainable exploitation. A central aspect of these projects was the establishment of a comprehensive monitoring system to track temperature variations over time within the aquifers. Through numerical modelling and operational data, the study highlights key challenges such as thermal short-circuit within the aquifer and seasonal imbalance between heating and cooling demands. The paper outlines mitigation strategies including installation of air-coolers or heaters, solar thermal recharge and integration with district heating/cooling networks. These case studies underscore the importance of flexible system design, continuous monitoring, and balanced thermal loads to ensure the long-term sustainability of shallow geothermal resources in urban settings.