Groundwater faces increasing pressure from mining and agricultural activities, raising major concerns about its quality. Yet, no pre-mining groundwater assessment has been conducted in the Bejaia district, despite the region’s strong mineral and agricultural potential. This study employs a tripartite index-based approach including groundwater quality assessment (Water Quality Index WQI and Heavy Metal Evaluation Index HEI), non-carcinogenic risk assessment (HQ and HI), and irrigation suitability assessment (SAR, RSC, %Na, MAR) in an agricultural area primarily influenced by significant Pb-Zn mineralization. Twenty-six groundwater samples were collected during the low-water period and analyzed for major ions and trace elements. ArcGIS software was used for the spatial distribution of the indices. WQI values ranged from 24.78 to 102.05, indicating poor to unsuitable groundwater quality in 54% of the samples. HEI values ranged from 0.01 to 147.83, with 27% of the samples showing high heavy metal pollution, with an extremely high value of 147.83 coinciding with Pb-Zn mineralized zones. Furthermore, a significant non-carcinogenic risk was identified in both children and adult groups, with greater vulnerability observed among children. Irrigation suitability indices confirmed the suitability of groundwater for agricultural use across the majority of samples. These findings provide an initial pre-mining seasonal groundwater quality reference for this region and are essential for identifying contaminated zones, mitigating health risks, and supporting sustainable management strategies to preserve the mineral and agricultural resources of the Bejaia district.