The installation of drainage ditches and removal of vegetation in preparation for vacuum harvesting alters the carbon dynamics of peatlands. However, we lack the measurements to understand the spatial distribution and environmental and substrate quality controls of carbon dioxide (CO2) and methane (CH4) emissions, as well as how these factors change over the 20–30 year extraction period. For three summers, we measured CO2 and CH4 emissions using the closed chamber method at three actively extracted peatlands near Drayton Valley, Alberta, ranging from 2 to 28 years since the start of extraction. Measurements were made in the ditches, and on segments of peat (fields) between adjacent ditches. Field emissions did not change with distance from ditches, likely due to the observed homogeneity of volumetric water content (VWC) and temperature across the fields. Understanding carbon dynamics in the ditches will be important, as they emitted on average two and 10 times, respectively, the amount of CO2 and CH4 per square meter of the fields. We found moderate to weak relationships between carbon emissions and soil temperature, VWC and ditch water level, though ditch emissions were significantly reduced when there was standing water present. Altering conventional site management, such as increasing ditch spacing, could substantially reduce CH4 emissions from the managed area. Emissions did not decrease with time since start of extraction. We suggest that Canadian emission factor calculations for land-based emissions consider both peat quality variations among sites, and a site's extraction duration, which has been important in other studies.