The study of nutrient fate in aquatic ecosystems is of paramount importance for environmental management and biodiversity conservation. This research aimed to assess the environmental fate of nutrients in the Karun River using the Aquatox model in 2023. Water sampling was conducted seasonally at 10 different points (40 samples in total) (80 km north to 40 km south), and phosphate and nitrate levels were measured using the Hach spectrophotometry method. Additionally, the parameters Dissolved Oxygen (DO), Electrical Conductivity (EC), pH, and Total Suspended Solids (TSS) were measured according to standard methods. Benthic sediment samples were collected using an Ekman grab. A light microscope was used for the identification and counting of benthic species. For modeling the fate of nutrients, two scenarios were considered: S1 (15% reduction in nutrients) and S2 (15% increase in nutrients). The results showed that the average biodiversity indices, including Shannon, Simpson, Camargo, and Brillouin, were 1.295, 0.585, 0.308, and 1.247, respectively, indicating relatively poor biodiversity in the Karun River ecosystem. Furthermore, the annual average concentrations of phosphate and nitrate were estimated to be 4.55 mg/L and 64.23 mg/L, respectively. The simulation results revealed that a 15% reduction in nutrient concentration led to an increase in biodiversity; the average Shannon index reached 1.48 in the nutrient reduction scenario and 1.01 in the concentration increase scenario. Furthermore, the values of GPP (Gross Primary Production) decreased from 314 g per square meter per year to 223 g in the nutrient reduction scenario, while GPP reached 453 g per square meter per year in the nutrient increase scenario. The Faunal Factor index also showed a gradual increase in the nutrient reduction scenario, and conversely, a decrease in the nutrient increase scenario. Overall, the results of this research indicated that a reduction in nutrients can contribute to decreased interspecific competition and increased biodiversity.