This study was carried out to evaluate the eutrophication risk associated with the nutrient flux from the Ghaghara river by using nutrient molar ratios and indicators for coastal eutrophication potential values. The concentration of ammonium (3–8 times), nitrate (3–10 times), and phosphate (3–4.5 times) in the Ghaghara river were higher than the reported value for the unpolluted rivers indicating the contribution from the anthropogenic sources. The dissolved nutrients concentration showed significant seasonal variations in the Ghaghara river system. The specific yield of nitrate-N, phosphate-P, and dissolved silica-Si from the Ghaghara river were 0.49, 0.03 and 0.96 tons km−2 yr−1 respectively. The average molar ratio for dissolved inorganic nitrogen (DIN)/Dissolved inorganic Phosphate (DIP) was above 16:1, indicated phosphate limitation in biological productivity. In contrast, an average molar ratio of Dissolved inorganic Silica (DSi)/DIN of 4.6 ± 4.4 favored the diatom growth in the Ghaghara river. The negative value of P-ICEP (-2.93 kg C. km−2day−1) indicated phosphate limitation in the Ghaghara river. The positive value of N-ICEP (1.71 kg C·km−2day−1) indicates an excess of nitrogen over silica transport from the Ghaghara river to the Ganga river, which can create an eutrophication problem in the Ganga river.