Heat is a naturally occurring, widespread groundwater tracer that can be used to identify flow patterns in groundwater systems. Temperature measurements, being relatively inexpensive and effortless to gather, represent a valuable source of information which can be exploited to reduce uncertainties on groundwater flow, and, for example, support performance assessment studies on waste disposal sites. In a lowland setting, however, hydraulic gradients are typically small, and whether temperature measurements can be used to inform us about catchment-scale groundwater flow remains an open question. For the Neogene Aquifer in Flanders, groundwater flow and solute transport models have been developed in the framework of safety and feasibility studies for the underlying Boom Clay formation as a potential host rock for geological disposal of radioactive waste. However, the simulated fluxes by these models are still subject to large uncertainties as they are typically constrained by hydraulic heads only. In the current study, we use a state-of-the-art 3D steady-state groundwater flow model, calibrated against hydraulic head measurements, to build a 3D transient heat transport model, for assessing the use of heat as an additional state variable, in a lowland setting and at the catchment scale. We therefore use temperature–depth (TD) profiles as additional state variable observations for inverse conditioning. Furthermore, a Holocene paleo-temperature time curve was constructed based on paleo-temperature reconstructions in Europe from several sources in combination with land surface temperature (LST) remotely sensed monthly data from 2001 to 2019 (retrieved from NASA’s Moderate Resolution Imaging Spectroradiometer, MODIS). The aim of the research is to understand the mechanisms of heat transport and to characterize the temperature distribution and dynamics in the Neogene Aquifer. The simulation results clearly underline advection/convection and conduction as the major heat transport mechanisms, with a reduced role of advection/convection in zones where flux magnitudes are low, which suggests that temperature is also a useful indicator in a lowland setting. Furthermore, the performed scenarios highlight the important roles of (i) surface hydrological features and withdrawals driving local groundwater flow systems and (ii) the inclusion of subsurface features like faults in the conceptualization and development of hydrogeological investigations. These findings serve as a proxy of the influence of advective transport and barrier/conduit role of faults, particularly for the Rauw fault in this case, and suggest that solutes released from the Boom Clay might be affected in similar ways.