AbstractOilseed rape (OSR, Brassica napus L.) is an important feedstock for biodiesel; hence, carbon dioxide (CO2), methane (CH4) and particularly fertilizer‐derived nitrous oxide (N2O) emissions during cultivation must be quantified to assess putative greenhouse gas (GHG) savings, thus creating an urgent and increasing need for such data. Substrates of nitrification [ammonium (NH4)] and denitrification [nitrate (NO3)], the predominant N2O production pathways, were supplied separately and in combination to OSR in a UK field trial aiming to: (i) produce an accurate GHG budget of fertilizer application; (ii) characterize short‐ to medium‐term variation in GHG fluxes; (iii) establish the processes driving N2O emission. Three treatments were applied twice, 1 week apart: ammonium nitrate fertilizer (NH4NO3, 69 kg‐N ha−1) mimicking the farm management, ammonium chloride (NH4Cl, 34.4 kg‐N ha−1) and sodium nitrate (NaNO3, 34.6 kg‐N ha−1). We deployed SkyLine2D for the very first time, a novel automated chamber system to measure CO2, CH4 and N2O fluxes at unprecedented high temporal and spatial resolution from OSR. During 3 weeks following the fertilizer application, CH4 fluxes were negligible, but all treatments were a net sink for CO2 (ca. 100 g CO2 m−2). Cumulative N2O emissions (ca. 120 g CO2‐eq m−2) from NH4NO3 were significantly greater (P < 0.04) than from NaNO3 (ca. 80 g CO2‐eq m−2), but did not differ from NH4Cl (ca. 100 g CO2‐eq m−2) and reduced the carbon sink of photosynthesis so that OSR was a net GHG source in the fertilizer treatment. Diurnal variation in N2O emissions, peaking in the afternoon, was more strongly associated with photosynthetically active radiation (PAR) than temperature. This suggests that the supply of carbon (C) from photosynthate may have been the key driver of the observed diurnal pattern in N2O emission and thus should be considered in future process‐based models of GHG emissions.