The Biskra region, one of the arid regions in North-East Algeria, has known remarkable agricultural development, necessitating additional mobilization of groundwater resources, which are almost the only source of water in the region. In the long term, this heavy mobilization may threaten the quantity and quality of groundwater. This study was carried out to gain a better understanding of groundwater quality in the Terminal Complex (TC) aquifer of the Biskra region, to determine the hydrogeochemical processes controlling water mineralization, and further to investigate the suitability of the groundwater for consumption. For this purpose, multivariate statistical analysis, based on compositional data analysis (CoDA), including robust PCA, cluster analysis (HCA), ilr-ion diagram, and correlation analysis as well as graphical approaches, was carried out on the hydrochemical results of forty-four (44) groundwater samples analysed by standard methods. The results showed that most groundwater parameters exceeded WHO-recommended safe limits for drinking water. Robust CoDA revealed three distinct processes controlling groundwater hydrochemistry: the first “carbonate link” [NO3−, HCO3−, pH] at the northern boundary, which was progressively replaced by the second link [Ca2+, Mg2+, SO42−], and the third “mineralization link” [Na+, Cl−, K+, EC, TDS], located on the Outaya, Biskra, Sidi Okba, and El-Houche axes. In addition, around 93% of samples were within the geochemical zone [SO42− +Cl− >CO32-- HCO3−], while only 7% fell within the [CO32− - HCO3−> SO42− + Cl−] zone, with the following chemical facies dominating: Ca–SO4 (52.27%), Ca–Mg–SO4 (22.72%), Na–Cl (20.45%), and Ca–HCO3 (4.56%). The modified water quality index (WQI) revealed five quality classes: excellent (9.10%), good (11.36%), poor (65.90%), very poor (11.36%), and unsuitable quality (2.28%), with an apparent deterioration in water quality from north to south, following the same direction of groundwater flow. Finally, the use of CoDA with isometric log-ratio plotting, for the first time in the study area, has enabled a more thorough and reliable assessment of the processes controlling groundwater quality, which is valuable for rationalizing pumping and can help decision-makers to plan current and future water resource management practices.