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. Plain Language Summary: Peat extraction for use in horticulture growing media contributes to peatland disturbance in Canada. In preparation for extraction, drainage ditches are dug to dry out the surface peat, and the vegetation is removed. These actions shift these sites from net stores of carbon, to net emitters, including the release of carbon dioxide (CO2) and methane (CH4), two powerful greenhouse gases. Few studies have quantified carbon emissions during the extraction period. To address this, we measured CO2 and CH4 emissions from actively extracted sites in Alberta, Canada for three summers, focusing on the spatial distribution and environmental controls of the emissions. We found that the drainage ditches were hotspots of emissions, emitting two and 10 times, respectively, the amount of CO2 and CH4 per meter squared of the non‐ditch portion of the site. We also found that emissions from the peat fields did not change with distance from the drainage ditches. More research is needed to better understand these water‐carbon interactions. Our work can support management practices that reduce these carbon emissions to help create a more sustainable industry. For example, we found that reducing the number of drainage ditches at a site could substantially reduce total methane emissions. Key Points: Drainage ditches emitted on average two and 10 times the amount of carbon dioxide and methane per square meter compared to the fieldsIncreasing drainage ditch spacing should be considered as a management strategy to substantially reduce CH4 emissionsLimited spatial variability in field carbon emissions, with no observed change with distance from the drainage ditches [ABSTRACT FROM AUTHOR]