Yuqiao Reservoir in Tianjin City was taken as an example in this paper, a two-dimensional hydrodynamic and nutrient transport model considering substance exchange across the sediment-water interface was developed. The effects of two different scopes of dredging on the temporal and spatial distribution of nitrogen and phosphorus nutrients in the reservoir under different water quality background were simulated based on calibrated parameters. The results demonstrated that: the established model could reliably simulate the dynamic release of nitrogen and phosphorus nutrient from lake sediment and its content under the combined influence from sediment release and external pollutant input; sediment was an important source of nutrients in Yuqiao Reservoir. The content of nitrogen and phosphorus nutrient in the reservoir would decreased after dredging, but different dredging schemes varied markedly. Dredging around the reservoir contributed much to water quality of shallow coastal waters but had little effect (<2%) on the whole reservoir. Dredging the whole reservoir resulted in a significant decrease (26%~48%) of nitrogen and phosphorus nutrients in the reservoir which showed a relatively obvious improvement on water quality.