<p>Urban rivers are hotspots for atmospheric CH₄ and CO₂ emissions. Monitoring their fluxes is of great significance for understanding the carbon cycle process disrupted by human activities and assessing the carbon budget of river basins. The emissions of greenhouse gases from natural rivers have been widely studied, but the impact of urbanization and land use changes caused by human activities on the distribution pattern of carbon fluxes in rivers around cities is still not fully understood. To bridge this knowledge gap, this study set up 14 sampling points with a total of 28 samples. By using the static flux chamber method, the fluxes of CH₄ and CO₂ in the Fen River, a tributary of the Yellow River, were determined, and the relevant physical and chemical indicators of the water body were monitored simultaneously. The results showed that both gases were in a supersaturated state, and the average values of FCH₄ and FCO₂ reached 1005.53 ± 459.16 μmol·m⁻²·d⁻¹ and 289.75 ± 176.45 mmol·m⁻²·d⁻¹, respectively. The FCH₄ of Wet month was 1.4 times that of Dry month, and the FCO₂ of Wet month was 2.4 times that of Dry month. The ratio of built-up area respectively explained 54% and 31% of the spatial variations of FCH₄ and FCO₂. The structural equation model indicates that the standardized direct effects of urbanization on FCH₄ and FCO₂ were 0.21 and 0.23 respectively, while the standardized indirect effects through physical and chemical indicators of water bodies (TP, DOC, NH₄⁺ and EC) were 0.47 and 0.40 respectively. Thus, nutrient inputs became the primary drivers for the increase in FCH₄ and FCO₂. This study suggests that FCH₄ and FCO₂ in river sections near urban areas are more sensitive to land-use changes and water pollution. Land use and urbanization indirectly affect riverine FCH₄ and FCO₂ by altering nutrient inputs. These findings underscore that FCH₄ and FCO₂ in river segments near urban areas are more sensitive to changes in land use and water pollution. Land use and urbanization indirectly influence riverine FCH₄ and FCO₂ by altering nutrient inputs. Such understanding is critical for future coordinated efforts aimed at pollution reduction and carbon mitigation along urban–rural river gradients, as well as for addressing the pressures of climate change.</p> Graphical Abstract <p></p>