Nowadays, the introduction of nutrients caused by human activities is considered an environmental issue and a significant problem in river basins and coastal ecosystems. In this study, the concentration of nutrients ( and ) in the surface water sources of the Maroon-Jarahi watershed in the southwest of Iran was determined, and the pollution status and health risk assessment were done. The average concentration of nitrate and phosphate in Ludab, Maroon, Zard, Allah, Jarahi rivers, and Shadegan wetland were obtained at 2.25–0.59, 4.59–1.84, 4.07–2.02, 5.40–2.81, 11.51–4.67, 21.63 and 6.20 (mg/l), respectively. A comparison of the results with the World Health Organization (WHO) limit showed that nitrate was lower than in all stations, but phosphate was higher than the limit in some stations of the Maroon, Allah, Jarahi rivers, and Shadegan wetland. Calculation of linear regression analysis showed significant positive relationships between nitrate and phosphate in all surface water sources (except Ludab) and based on the N/P ratio, nitrogen was estimated as the limiting factor in phytoplankton growth (N/P < 16). The evaluation of the status of the Nutrient pollution index (NPI) was observed as: Shadegan > Jarahi > Allah > Maroon > Zard > Ludab that the Jarahi River and Shadegan wetland were in the medium pollution class (1 < NPI ≤ 3) and other waterbodies were in the non-polluted to low pollution state (NPI < 1). Calculation of the chronic daily intake (CDI) showed that water body nutrients cause more non-carcinogenic health risks through the oral route than dermal exposure, and according to HI, children's health is more at risk than adults. Findings showed that surface water resources especially downstream of the Maroon-Jarahi watershed are at eutrophication risk, and to control the nearby human activities and as a result increase the nutrients in these water resources, measures should be taken.