Agriculture systems are becoming a growing concern regarding greenhouse gas (GHG) emissions; specifically, methane (CH4), carbon dioxide (CO2) and nitrous oxide (N2O). This study focused on GHG transport within two controlled tile drained agriculture sites in Eastern Ontario. Subsurface and surface greenhouse gas fluxes were monitored throughout a transect at each site with sampling locations in the farm field and the shoulder and slope of the riparian zone in the fall of 2017 and the 2018 agronomic season. All sampling locations showed similar levels of CO2 and N2O emissions; however, CH4 is observed as effluxes in oxidizing soils and influxes in reducing soils. GHG transport increases as soil depth decreases with maximum fluxes occurring at the soil/atmosphere interface. GHG transport is elevated in soil horizons that display larger concentration gradients and lower water saturation levels. Surface emissions are primarily influenced by GHGs produced and transported in shallow soil horizons.