Shallow geothermal systems are the most efficient and clean technology for the air-conditioning of buildings and constitutes an emergent renewable energy resource in the worldwide market. Undisturbed systems are capable of efficiently exchanging heat with the subsurface and transferring it to human infrastructures, providing the basis for the successful decarbonisation of heating and cooling demands of cities. Unmanaged intensive use of groundwater for thermal purposes as a shallow geothermal energy (SGE) resource in urban environments threatens the resources' renewability and the systems' performance, due to the thermal interferences created by a biased energy demand throughout the year. The exploitation regimes of 27 groundwater heat pump systems from an alluvial aquifer were firstly examined using descriptive statistics. Linear relationships between abstraction and injection temperatures of the systems were assessed by calculating Pearson's r correlation coefficient, and used as an evidence of thermal interferences. Then, time series of flow rate, operation temperature and energy transfer were modelled by means of spectral analysis and sinusoidal regression methods, followed by the definition of the relative exploitation patterns. The exploitation regimes examined presented a clear cooling bias and a similar cyclicality. The amplitudes correlated with the different end-user's activities (e.g. medical centres) when high frequency cycles were observed, while climatization strategies (e.g. constant flow rates and modulation of injection temperatures) did so when low frequency cycles were detected. The time series models allowed defining the relative operational pattern of a system and the groups of systems following such patterns. The biases in exploitation regimes of groundwater heat pump systems existing in Mediterranean areas require correction measures to ensure a more balanced exploitation of the SGE resources. The definition of the characteristic exploitation pattern proposed could be applied to guide resource managers by identifying unbalanced systems, understanding existent exploitation strategies and proposing corrective alternative plans.