Geochemical data from the deep aquifer system below the Boom Clay in NE-Belgium have been collected and reinterpreted. The data were obtained between 1980 and 2014 within the framework of radioactive waste disposal studies. Currently, groundwater in the deep aquifer system mainly ranges between NaHCO3 type and NaCl type. Because of the low groundwater velocity in this aquifer system, re-equilibration with the mineralogical composition of the host formations generally occurs. The main geochemical indicators point out that the current formation waters are a mixture between the original saline marine porewaters and freshwater recharge. SE-NW gradients of increasing ion concentrations are observed and can be explained in agreement with the pattern of natural groundwater flow. Calcite dissolution and cation exchange are still ongoing in this freshening aquifer system. A low sulphate content in the deep aquifer system indicates sulphate reduction associated with organic matter degradation. Inverse modelling along a flow path using PHREEQC generally confirms the reactions that have been derived in the data analysis.