Rivers are widely reported as CO₂-emitting hotpots and are attracting increasing attention worldwide. However, less attention has been given to the CO₂ emission from the suburban rivers which are experiencing rapid watershed urbanization and increasing anthropogenic stress. Here, two small suburban rivers in Southwest China were studied, and seasonal sampling campaigns with high spatial resolution were carried out to explore the characterization of partial pressure (pCO₂) and CO₂ efflux and their possible controls. The results showed that, the pCO₂ and estimated CO₂ fluxes from the two suburban rivers ranged from 37 to 6466 μatm (mean of 1293 ± 1126 μatm) and −72–1569 mmol·m⁻²·d⁻¹ (mean of 185 ± 240 mmol·m⁻²·d⁻¹), respectively. And, both of them exhibited disproportionately high variability and acted as strong CO₂ emitters to the atmosphere. The pCO₂ in the two suburban rivers showed significant spatial variability, with urban sections having 2–2.5 times higher values than exurban sections, and, the urban land use proportion in the basins accounted for 35%–67% of such spatial variation in pCO₂. The sewage-dominated urban tributaries had much higher pCO₂ and acted as an obvious exciter to the high pCO₂ in urban sections of suburban rivers. Carbon and nutrients concentrations also accounted for the spatial variation in pCO₂ and fCO2 in the two suburban rivers, and acted as good indicators. The seasonal variation in pCO₂, with the highest values in autumn and lowest values in spring, was controlled by the precipitation dilution effect and seasonal temperature as well as the boosted primary production at several urban sites. We highlighted that small suburban rivers showed disproportionally high spatial variability in pCO₂ and CO₂ fluxes in their limited basin areas due to the development of urbanization, and could be used as a good model for studying the complex impacts of anthropogenic disturbances on river carbon biogeochemical processes.