Surface samples and depth profiles of carbon dioxide and methane concentrations were sampled from 2015 to 2023 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 surface samples were collected at a gauged weir on Falling Creek Reservoir's primary inflow tributary, from a wetland adjacent to Falling Creek Reservoir, and from the reservoir outflow. At Beaverdam Reservoir, additional samples were collected at three outflow points below the dam and at the mid-reservoir outflow. Samples were collected approximately fortnightly from March-April, weekly from May-October, and monthly in November-February 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 (see site descriptions file for geographic coordinates of sampling sites).