Growing evidence shows that water networks in agricultural watersheds, including rivers, paddy fields (PFs), and ditches (DCs), are hotspots of aquatic greenhouse gas emissions globally. However, the knowledge of the role of natural processes and anthropogenic activities, including agricultural practices, in promoting CO 2 production and emissions still remains unclear. In this study, sampling and analysis of different surface waters during the agricultural drainage period were conducted to clarify the production mechanism and emission of CO 2 . The results showed that all of the surface waters in the Nongjiang River (NJR) watershed acted as sources with respect to atmospheric CO 2 , while a few in the Honghe Wetland and the estuary acted as CO 2 sinks. Longitudinal variations of CO 2 in mainstreams of the NJR indicated that fertilizer application, manure, and sewage discharges stimulated the CO 2 production, while those in the Yalu River (YLR) were mainly affected by the natural wetlands. The accumulation of carbon and nitrogen in waters of PF and DC have enhanced CO 2 emissions during drainage periods. The high ratio of ΔCO 2 /ΔO 2 revealed the important role of the extensive respiration in CO 2 production in the NJR. Furthermore, the correlation between dissolved oxygen and CO 2 demonstrated that respiration and photosynthesis dominated CO 2 production and consumption in all types of water bodies. This study implied that agricultural water networks might be vague sources for aquatic systems, and effort is still urgently needed to quantitatively assess the CO 2 emissions in the context of wetland−farmland shifts regionally and worldwide.