Abstract. The assessment of cropland carbon and nitrogen (C and N) balances plays a key role in identifying cost-effective mitigation measures to combat climate change and reduce environmental pollution. In this paper, a biogeochemical modelling approach is adopted to assess all C and N fluxes in a regional cropland ecosystem of Thessaly, Greece. Additionally, the estimation and quantification of the modelling uncertainty in the regional inventory are realized through the propagation of parameter distributions through the model, leading to result distributions for modelling estimations. The model was applied to a regional dataset of approximately 1000 polygons, deploying model initializations and crop rotations for the five major crop cultivations and for a time span of 8 years. The full statistical analysis on modelling results (including the uncertainty ranges given as ± values) yields for the C balance carbon input fluxes into the soil of 12.4 ± 1.4 t C ha−1 yr−1 and output fluxes of 11.9 ± 1.3 t C ha−1 yr−1, with a resulting average carbon sequestration of 0.5 ± 0.3 t C ha−1 yr−1. The averaged N influx was 212.3 ± 9.1 kg N ha−1 yr−1, while outfluxes of 198.3 ± 11.2 kg N ha−1 yr−1 were estimated on average. The net N accumulation into the soil nitrogen pools was estimated to be 14.0 ± 2.1 kg N ha−1 yr−1. The N outflux consists of gaseous N fluxes composed of N2O emissions of 2.6 ± 0.8 kg N2O–N ha−1 yr−1, NO emissions of 3.2 ± 1.5 kg NO–N ha−1 yr−1, N2 emissions of 15.5 ± 7.0 kg N2–N ha−1 yr−1 and NH3 emissions of 34.0 ± 6.7 kg NH3–N ha−1 yr−1, as well as aquatic N fluxes (only nitrate leaching into surface waters) of 14.1 ± 4.5 kg NO3–N ha−1 yr−1 and N fluxes of N removed from the fields in yields, straw and feed of 128.8 ± 8.5 kg N ha−1 yr−1.