In the Reggane arid region, the Continental Intercalaire (CI) aquifer plays a critical role as a water source, meeting daily water needs such as drinking, domestic use, and agricultural usage. This study assessed the hydrogeochemical characteristics influencing water mineralization, the overall quality of the groundwater in the CI aquifer for consumption and irrigation usage, and identifies possible chronic health risks for different age groups. To this end, groundwater samples were collected and analyzed for various physicochemical parameters. The assessment tools used include graphical plots, statistical analyses, groundwater pollution index (GPI), nitrate pollution index (NPI), health risk assessment (HRA) model, and irrigation water quality index (IWQI). GPI analysis reveals that 16%, 40%, and 44% of CI aquifer samples are classified with moderate, high, and extremely high pollution, respectively. The NPI method indicates that nitrate pollution levels fall into three categories: moderate (12%), significant (36%), and very significant (49%). HRA results showed that human health risks varied between 3.13 and 10.46 for children, 2.47 and 8.27 for teenagers, and 1.61 and 5.38 for adults, signifying an high risk that spanned all age demographics in the region. Regarding agricultural use, IWQI indicates that water from all studied wells is highly unsuitable for irrigation, potentially harming both soils and plant growth. Hydrochemical analysis by Piper diagram suggested a water type evolution from Na-Cl upstream to Ca-Mg-Cl downstream. Other analytical tools, like Gibbs diagrams, scatter plots, chloro-alkaline indices, saturation indices and multivariate statistical tools, indicated that the hydrochemistry is mainly influenced by interactions with aquifer materials, notably silicate weathering, halite and gypsum dissolution, and cation exchange processes. The study also revealed that the presence of nitrates is primarily attributable to domestic effluents from residential areas.