This study investigates the decades-long evolution of groundwater dynamics and thermal field in the North German Basin beneath Brandenburg (NE Germany) by coupling a distributed hydrologic model with a 3D groundwater model. We found that hydraulic gradients, acting as the main driver of the groundwater flow in the studied basin, are not exclusively influenced by present-day topographic gradients. Instead, structural dip and stratification of rock units and the presence of permeability contrasts and anisotropy are important co-players affecting the flow in deep seated saline aquifers at depths >500 m. In contrast, recharge variability and anthropogenic activities contribute to groundwater dynamics in the shallow (<500 m) freshwater Quaternary aquifers. Recharge fluxes, as derived from the hydrologic model and assigned to the parametrized regional groundwater model, reproduce magnitudes of recorded seasonal groundwater level changes. Nonetheless, observed instances of inter-annual fluctuations and a gradual decline of groundwater levels highlight the need to consider damping of the recharge signal and additional sinks, like pumping, in the model, in order to reconcile long-term groundwater level trends. Seasonal changes in near-surface groundwater temperature and the continuous warming due to conductive heat exchange with the atmosphere are locally enhanced by forced advection, especially in areas of high hydraulic gradients. The main factors controlling the depth of temperature disturbance include the magnitude of surface temperature variations, the subsurface permeability field, and the rate of recharge. Our results demonstrate the maximum depth extent and the response times of the groundwater system subjected to non-linear interactions between local geological variability and climate conditions.