Apparent groundwater age dating has been proven useful and robust in understanding water origin and mixing processes, particularly when multiple tracers are considered. However, even though now extensively used, the age tracers have not been widely applied in the general practice of flow and transport model calibration. A multi tracer-study was carried out in the Neogene aquifer in Flanders to quantify the apparent age and construct a joint interpretation for the delineation of different groundwater flow systems. This understanding is critical as part of the safety and feasibility studies for the underlying Boom Clay Formation that has been considered as a potential host rock for the geological disposal of radioactive waste. In this study, we combine evidence from tritium/helium-3 (3H/3He), helium-4 (4He) and radiocarbon (14C) dating as well as stable isotopic (δ18O, δ2H) and hydrochemical signatures in combination with particle tracking-based age distributions from the 3D groundwater flow model. The results of the study indicate that mixing of groundwater with young and old fractions occurs predominantly in the central part of the aquifer which is made evident by the coexistence of 3H (pre and post-bomb pulse Era), 14C and 4He in several groundwater samples. The mixing between water of different origin is also supported by the sampled stable isotopic and hydrochemical composition of groundwater. Particle tracking residence time results show an acceptable agreement with apparent ages derived from age tracers for young (≤100 years) and old (>1000 years) groundwater. Groundwater with ages between 100 and 1000 years is likely a mixture of water with young/old fractions and shows the strongest discrepancies between advective model ages and age tracer based apparent ages. On the basis of our findings, we distinguish between three groundwater flow systems in the Neogene aquifer: i) a shallow/local flow system, with groundwater originating from modern meteoric water; ii) a deep/semi-regional flow system, characterized by old groundwater where the presence of 4Herad is significant; iii) a mixed zone of groundwater flow where the recently infiltrated meteoric water mixes with discharging old groundwater. These results have helped us to refine previously proposed conceptual models for the study area and will in the end reduce uncertainties relevant to the potential future geological disposal of radioactive waste.