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Abstract Deep tropical soils with net anion exchange capacity can adsorb nitrate and might delay the eutrophication of surface waters that is often associated with many temperate croplands. We investigated anion exchange capacity and soil nitrate pools in deep soils in the Southern Brazilian Amazon, where conversion of tropical forest and Cerrado to intensive fertilized soybean and soybean-maize cropping expanded rapidly in the 2000s. We found that mean soil nitrate pools in the top 8 m increased from 143 kg N ha⁻¹in forest to 1,052 in soybean and 1,161 kg N ha⁻¹in soybean-maize croplands. This nitrate accumulation in croplands aligned with the estimated N surpluses in the croplands. Soil anion exchange capacity explained the magnitude of nitrate accumulation. High nitrate retention in soils was consistent with current low levels of streamwater nitrate exported from croplands. Soil exchange sites were far from saturation, which suggests that nitrate accumulation can continue for longer under current cropping practices, although mechanisms such as competition with other anions and preferential water flowpaths that bypass exchange sites could reduce the time to saturation.