Depth profiles of carbon dioxide and methane concentrations were sampled during the ice-free period from 2016 to 2018 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. The samples were collected approximately fortnightly from March-April, weekly from May-October, and monthly in November at Falling Creek Reservoir and Beaverdam Reservoir.