Vegetation management and dredging of agricultural drainage ditches are practices often necessary to improve field drainage. However, these practices can influence soil greenhouse gas (GHG) emissions in and around the drainage ditches by influencing, for instance, soil/sediment profiles, water/air temperatures, plant nutrient uptake, and hydrology (soil). In this study, surface GHG fluxes (CO2, CH4, N2O) were compared between a vegetation brushed + dredged (managed) agricultural drainage ditch and an adjacent ditch that was not brushed or dredged (control), in eastern Ontario, Canada, during three growing seasons (2018–2020). Fluxes were measured on ditch shoulders, midslopes, hyporheic zones, and channel areas. Soil CO2 emissions increased (15–40%) along the managed ditch after trees were removed, in relation to the control ditch and this increase was likely due to warmer temperatures (3°C) and increased soil microbial activity as a result of decreased shading effects. And, moreover, the rapid natural re-establishment of shrubs and grasses after initial woody vegetation brushing did not cause substantial change in fluxes, in relation to time periods immediately following ditch management intervention. In-stream CH4 emissions after dredging were lower (> 90%). CO2 and CH4 were the dominant GHGs fluxes (20-yr CO2eq) in the riparian areas of the drainage ditches, with N2O emissions being significantly smaller (1–3%).