Under the influences of fertilization and soil leaching, the source and sink effects of methane (CH4) in surface waters of agricultural watersheds remain unclear. Currently, the monitoring and studying of CH4 emissions in waters of agricultural watersheds are still inadequate. This study focused on the Nongjiang River Basin within the Sanjiang Plain, employing the headspace equilibrium method and the diffusion model approach to precisely monitor and estimate the CH4 concentrations and fluxes in various water bodies of the basin. The results showed that the water bodies in the Nongjiang watershed generally acted as sources of atmospheric CH4. The CH4 fluxes at the water-air interfaces of the Yalü River, Nongjiang River, ditches, and paddy fields ranged from 0.51 to 99.60, 0.97 to 20.44, 4.13 to 20.90, and 24.84 to 58.07mg/(m2.d), respectively. The CH4 fluxes from ditches and paddy fields were 2 and 7 times higher than those of the Nongjiang River, respectively. In the Yalü River and ditches, CH4 concentrations correlated significantly and negatively with pH and dissolved oxygen (DO), while the CH4 concentrations in the Nongjiang River correlated significantly and positively with DO. The CH4 concentrations in the Nongjiang River and ditches water bodies were significantly positively correlated with dissolved organic carbon (DOC), indicating that the use of agricultural organic fertilizer during the drainage period promotes the production of CH4. The study found that river reaches that flow through shallow wetlands and agricultural areas generally have higher CH4 concentrations and fluxes, suggesting the effects of land use patterns on CH4 emissions were important. Compared with other agricultural watersheds globally, the Nongjiang River during the drainage period has higher CH4 concentrations and lower CH4 fluxes, low wind speed eased the CH4 diffusion at water-air interface; while the the low CH4 flux in the ditch waters during the drainage period mainly resulted from the high DO. As a typical agricultural area in the northeastern black soil region of China, understanding the production and emission of CH4 in the agricultural watersheds is of great significance for future carbon budget balances and carbon emission assessments in this region. © 2024 Chinese Society for Environmental Sciences. All rights reserved.