Urban aquatic ecosystems in plains are often subject to extensive anthropogenic pollutant inputs and have prolonged times for pollutant degradation, potentially leading to diverse carbon emission patterns. This study explored carbon emission patterns and underlying mechanisms in Ge Lake and its tributaries, located in an urban area within a plain in China. The results revealed that carbon emissions from rivers were significantly higher than those from the downstream lake. Spatial interpolation analysis further revealed that CO2‐eq emissions from a 1‐km2 river area can be equivalent to those from an area as large as 86‐km2 of the downstream lake. Rivers are the gateway for the entry of organic compounds, often carrying substances that are readily biodegradable. As the river water moves slowly, these compounds accumulate and undergo degradation in rivers before they reach downstream lakes. The findings may benefit the estimates of carbon emissions in these regions with greater precision. Plain Language Summary Carbon dioxide (CO2) and methane (CH4) are the two most important greenhouse gases. Inland waters are hotspots of CO2 and CH4 emissions, greatly contributing to atmospheric levels. This study investigated the patterns of CO2 and CH4 emissions from aquatic ecosystems within plains, known for high pollutant loads and extended residence times. The results revealed that CO2 and CH4 emissions from rivers were significantly higher than those from the downstream receiving lake, exhibiting a decrease along the river flow direction. Rivers serve as the gateway for the entry of pollutants to aquatic environments, often carrying substances that are readily biodegradable. As the river water moves slowly, these compounds accumulate and undergo degradation in rivers before they reach downstream lakes, and therefore, CO2 and CH4 emissions diminish in the downstream direction. The findings add the understanding of carbon emissions in plain aquatic ecosystems, and benefit their estimates in these regions with greater precision. Key Points Carbon emissions from urban rivers were higher than the downstream receiving lake Carbon emissions exhibited a decreasing trend along the river flow direction Urban rivers warrant more attention in regional estimates of carbon emissions