Several management strategies, such as wastewater treatment plants (WWTPs), have been increasingly used to mitigate nutrient pollution at watershed scale during the past few years. However, their cost-efficiency in controlling nutrient load is still debatable. This study quantified the annual cost of WWTP and constructed wetland based on process-based modeling of nutrient dynamics within a typical lowland rural watershed in Eastern China. The evaluation results revealed that constructed wetland with macrophyte coverage increased by 10% and 15% can result in an identical reduction of nitrogen and phosphorus load by WWTP. However, a cost analysis revealed that the strategy of WWTP had a higher annual cost (65,538 Yuan/yr) compared with the strategy of constructed wetland with an annual cost of 24,012 Yuan/yr. The case study revealed that WWTPs are not necessarily cost-effective for controlling nutrient load from China’s lowland rural areas. This is because WWTP is costly, while constructed wetland based on the widely-distributed pond ecosystems in lowland areas can save considerable investments. We concluded that an adequate cost-effectiveness evaluation for management strategies in nutrient removal will benefit our decision-making.