Recently, agricultural land use has significantly impacted carbon emissions and water quality in adjacent rivers. This study examined the influence of land-use types and seasonality on carbon emissions from agriculture-impacted rivers in Shanghai. Our results showed that the crop farming land-use-associated river (AR) had CH4 and CO2 fluxes 2.68 and 3.47 times higher, respectively, than those in the aquaculture land-use-AR and 2.86 and 2.81 times higher than in the livestock and poultry breeding land-use-AR. Statistical analyses revealed that total nitrogen, ammonia nitrogen, and humification index were significantly correlated with crop farming land-use-AR carbon emissions. Conversely, no clear correlation was found between chemical factors and carbon fluxes in the aquaculture land-use-AR and livestock and poultry breeding land-use-AR due to the complexity of pollution sources. Seasonality significantly influenced CH4 and CO2 fluxes from agriculture-impacted rivers, with carbon fluxes in summer being 3.5 and 2.5 times higher than in winter, respectively. Crop farming land-use-AR carbon fluxes exhibited the highest variability under seasonal influences. This study emphasizes the need for policies to mitigate agricultural land use impacts on river carbon emissions.