Dams impact a significant portion of the world's rivers, and rivers downstream of the reservoirs created by large dams often emit significant amounts of methane (CH4). River CH4 emissions downstream of run‐of‐the‐river (ROR) dams are less well known. We investigated spatial and seasonal CH4 dynamics along a stretch of the Aare River (Switzerland) downstream from a bubbling ROR reservoir. We found that the CH4 horizontally accumulated in this vertically non‐stratifying ROR reservoir was consistently transported to the downstream river, but half was lost near a confluence with a tributary. We estimated CH4 diffusion using gas exchange coefficient (k) models that incorporate specific river characteristics and found CH4 emissions were threefold higher upstream of the confluence than downstream. We discuss the use of CO2‐derived k models in estimating k for CH4, and investigated it directly using a drifting chamber experiment. While chamber emissions only partly agreed with the k models, the models were robust enough to use in a CH4 mass balance along the river that indicated an overall CH4 loss from the study area. The loss predominantly occurred at the confluence and > 92% of it could not be accounted for by modelled or measured CH4 emissions. Ultimately, a ROR reservoir that does not form an anoxic, CH4‐rich hypolimnion enhanced downstream river CH4 emissions, but to a lesser extent than other systems (∼9% of total reservoir‐associated emissions). Regardless, small ROR dams and river features such as confluences should be considered when measuring, estimating or upscaling river CH4 emissions.