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Anthropogenic activities causing a transformation of the natural nitrogen and phosphorus cycle are considered as one of the most fundamental environmental issues. In this study, nitrate and phosphate concentrations in waterbodies such as Abadaba river, Agulu lake, Njaba river, Oguta Lake, and Nike Lake located in Southeast, Nigeria was determined in both dry and wet season by spectrophotometric technique and modeled for pollution and health risks assessment. Result revealed that nitrate ranged from 13.163±2.30 mg/L at Nike to 36.173±7.22 mg/L Oguta lake in dry season while in the wet season it ranged from 17.402±3.459 mg/L at Abadaba to 26.748±6.536 mg/L at Njaba river. Phosphate ranged from 2.144±0.513 mg/L at Nike to 9.741±3.207 mg/L at Oguta in dry season while from 36.330±7.420 mg/L at Abadaba to 40.204±6.024 mg/L at Oguta. Comparing results with World Health Organization (WHO) allowed limits, it revealed that nitrate was low while phosphate was only low in the dry season at Abadaba, Agulu and Oguta lake. The waterbodies showed low variations (< 20 %) with positive linear relationships (R2 ≥ 0.3) for both nitrate and phosphate in both dry and wet season. Furthermore, except at Abadaba and Agulu in the dry/wet season and Njaba and Oguta in wet season, which showed no significant differences (p > 0.05) between them, all other showed significant difference (p < 0.05) for nitrate and phosphate concentrations. In terms of season, only at Njaba (for phosphate only) showed no significant differences (p > 0.05), all others waterbodies showed significant differences (p < 0.05) in nitrate and phosphate concentration in both seasons. The nitrate to phosphate ratio was very low especially in the wet season due to the high input of phosphate. The nutrient pollution index showed moderate to very high pollution while the waterbodies will pose very high non-carcinogenic health risks to users via the oral pathway. Overall, the waterbodies are at risk of eutrophication and efforts should be put in place to reduce anthropogenic activities around the area and thus input of nutrients in these water bodies.