The impoundment of running waters through the construction of large dams is recognised as one of the most important factors determining the transport, transformation, and outgassing of carbon (C) in fluvial networks. However, the effects of small and very small water retention structures (SWRS) on the magnitude and spatiotemporal patterns of C emissions are still unknown, even though SWRS are the most common type of water retention structure causing river fragmentation worldwide. Here we evaluated and compared diffusive carbon dioxide (CO2) and methane (CH4) emissions from river sections impounded by SWRS and from their adjacent free-flowing sections along a highly impounded river. Emissions from impounded river sections (mean [SE] = 17.7 [2.8] and 0.67 [0.14] mmol m−2 d−1, for CO2 and CH4, respectively) never exceeded those from their adjacent free-flowing river sections (230.6 [49.7] and 2.14 [0.54] mmol m−2 d−1). We attribute this finding to the reduced turbulence in impounded river sections induced by SWRS compared to free-flowing river sections (i.e., physical driver). Likewise, the presence of SWRS favoured an increase of the concentration of CH4 in impounded waters, but this increase was not sufficient to cause a significant influence in the CH4 efflux from the downstream free-flowing river sections. By contrast, this influenced the larger-scale longitudinal patterns of dissolved CH4, which exhibited a clear shifting pattern along the study stretch, modulated by variables associated with the presence of SWRS, such as higher water residence times, higher sedimentation rates, and higher temperatures. Overall, our results show that the presence of SWRS can modify the concentrations of C gases in highly impounded rivers but exerts a minor influence on diffusive C emissions.