Diffusive fluxes of methane and carbon dioxide were measured using an Ultraportable Greenhouse Gas Analyzer (UGGA) in Falling Creek Reservoir (FCR) and Beaverdam Reservoir (BVR; Vinton, Virginia, USA). FCR and BVR are owned and operated by the Western Virginia Water Authority as drinking water sources for Roanoke, Virginia. The dataset consists of calculated diffusive fluxes of methane and carbon dioxide measured at the deepest site of the reservoir adjacent to the dam (2018–2021) and additional upstream sites in FCR (2018). Measurements were collected approximately fortnightly in FCR throughout the stratified periods of 2018–2021, while measurements from BVR were only taken in 2018.