Surface samples and depth profiles of carbon dioxide and methane concentrations were sampled during the ice-free period from 2015 to 2020 in two drinking water reservoirs in southwestern Virginia, USA: Beaverdam Reservoir (Vinton, Virginia) and Falling Creek Reservoir (Vinton, Virginia). Both reservoirs are owned and operated by the Western Virginia Water Authority as primary or secondary drinking water sources for Roanoke, Virginia. The dataset consists of depth profiles of dissolved greenhouse gas (carbon dioxide, methane) samples measured at the deepest site of each reservoir adjacent to the dam. Additional samples were collected at a gauged weir on Falling Creek Reservoir's primary inflow tributary as well as surface samples from a wetland adjacent to Falling Creek Reservoir. At Beaverdam Reservoir, additional samples were collected at the outflow below the dam. Samples were collected approximately fortnightly from March-April, weekly from May-October, and monthly in November at Falling Creek Reservoir and Beaverdam Reservoir. In 2019, surface samples along the stream and reservoir continuum from both Falling Creek Reservoir and Beaverdam Reservoir were collected monthly during the summer stratified period.