Calculations of nitrogen (N) budgets can help in the understanding of agroecosystem functioning and in proposing more sustainable management strategies. Changes in the main N fluxes of the pampean agroecosystems of Argentina were calculated over time. The impact of management changes on regional N budget and possible future trends were estimated. Changes in land use were quantified using national censuses data. Biological N fixation of leguminous forages was assessed using a regression model and local field experimental data. Nitrogen fixation by soybean, the most extensive grain crop, was calculated using an existing model. Fertilizer input was based upon farmer surveys, and atmospheric N input estimated using local data. Nitrogen output by grain harvest was estimated using national yield statistics and averaged grain N concentration derived from many field experiments widespread over the region. During the last 50 years cropped area has doubled as a result of the widespread adoption of soybean as the main component of rotations. The agricultural expansion included areas previously used for grazing on seeded pastures and seasonal graminaceus forages. The historical N budget of the entire region was positive but has dropped from 2.0Mty−1 in 1960 to 1.3Mty−1 at present. This reduction implies that N fixation by soybean and fertilizer application were lower than the previous livestock/pasture systems N input. During the cropping phase of rotations the N budget was usually negative in the past. Currently, in low yielding areas of semiarid environments, the N budget turned positive; meanwhile in humid climates with high productivity scenarios it remained negative. Fertilizer rates applied balanced N output in the former case but not in the latter. Partial factor productivity of N inputs increased from 3- to 6-fold during the last 50 years in the Pampas. Uncertainties related to the estimations performed are discussed.