In this study, we discussed the impacts of human water consumption to the nutrient burden in a river estuary, and used Huanghe River as a case study. The agricultural water consumption from the Huanghe River has significantly decreased the natural water flows, and the amount of water consumption could be almost twice as high as the water entering into the estuary. According to our calculation, agricultural water usage decreased TN outflows by 6.5 x 104 Mg/year and TP outflows by 2.0 x 103 Mg/year. These account for 74% and 77% of the total output loads. It has been widely reported that the majority of the rivers in northern China were severely polluted by nutrients. Its implication on the budget of nutrient in the estuary ecosystem is not well characterized. Our study showed that the discharge of nutrients in the coast waters from polluted rivers was over concerned. Nutrients in the polluted rivers were transported back to the terrestrial systems when water was drawn for human water consumption. The magnitudes of changes in riverine nutrient discharges even exceed the water-sediment regulation trails in the Huanghe River. It has non-negligible impact on estimating the nutrient burden in costal water ecosystem.