This study was carried out to investigate the current status of surface water and groundwater quality in Lower Seybouse and Annaba Plain, NE Algeria. 36 surface water and groundwater samples were collected in this area, and various physicochemical parameters were analysed. The quality of surface water and groundwater for drinking and the associated health risks were assessed using a Water Quality Index (WQI) and a Human Health Risk Assessment (HHRA) model. The results show that all samples are alkaline with the EC values ranging from 1139 to 5555 μS/cm. The ionic dominance pattern was in the order of Na+ > Mg2+ > Ca2+ > K+ for cations and Cl– > HCO3– > SO42 – > NO3– for anions, respectively. The dominant water types are SO4-Cl-Ca-Mg and SO4-Cl-Na, formed by dissolution of evaporative and carbonate-rich material. All samples are unsuitable for drinking, with 1 sample classified as poor (rank = 4) and 35 samples as extremely poor (rank = 5). These samples are mainly located near the Seybouse Wadi, which is a natural outlet for wastewater from human activities. The assessment of non-carcinogenic risk showed that the Hazard Index (HI) for males ranged from 0.12 to 1.01 with a mean of 0.30 and only one sample exceeded value 1. For females, the HI was between 0.16 and 1.28 for females, with a mean of 0.39. The risk for children was even higher, ranging from 0.41 to 3.28, with a mean of 1.03, suggesting that children are more vulnerable to water contamination. The Carcinogenic Risk (CR) values for Pb ranged from 10–3 to 8.6 · 10–3, with a mean of 2.6 · 10–3 for males, and between 1.4 · 10–3 to 10–2, with a mean of 3.3 · 10–3 for females, while for children the CR values ranged from 3.5 · 10–3 to 2.7 · 10–3, with a mean of 8.4 · 10–3, indicating that no possible CR from water drinking.