As the main channel for the drainage of paddy fields, the water quality of canals directly affects the water quality of surrounding water bodies. Factors such as rainfall and the release of accumulated pollutants from the sediment of the canals have a direct impact on the water quality of drainage ditches. Based on the measured hydrological and water quality data, a dynamic water quality model was built to simulate the runoff and water quality changes in a paddy field for different return periods (1, 2, 5, 10, 20, and 50 years), and to consider the effects of released drainage sediment on the water quality of the paddy field. The change in water quality in paddy fields and ditches in different periods was studied. The simulation results showed that under different return periods, the total nitrogen concentration and total phosphorus concentration in the water of the paddy field and ditch increased first, and then decreased with time in June and July–September, while the pollutant concentration remained basically stable after the end of rainfall. With the increase in return period, the total nitrogen concentration and total phosphorus concentration decreased gradually. The release of nitrogen and phosphorus from the sediment of ditches resulted in an increase in the total nitrogen concentration and total phosphorus concentration in the ditches, and an increase in the pollution load. Under the influence of rainfall and fertilizer, the total nitrogen concentration and total phosphorus concentration in paddy ditch drainage were generally higher and more polluted in June than in July–September, and under the influence of released sediment, the ditch drainage was most polluted in June when the return period was one year, with the total nitrogen concentration and total phosphorus concentration at the outlet of the paddy ditch reaching 21.63 mg/L and 0.88 mg/L, respectively. The research results can provide a theoretical basis and basic support for the interception and treatment of non-point source pollution in farmland.