Changes in precipitation in the Amazon Basin resulting from regional deforestation, global warming, and El Niño events may affect emissions of carbon dioxide (CO2), methane (CH4), nitrous oxide (N2O), and nitric oxide (NO) from soils. Changes in soil emissions of radiatively important gases could have feedback implications for regional and global climate. Here, we report the final results of a 5-year, large-scale (1 ha) throughfall exclusion experiment, followed by 1 year of recovery with natural throughfall, conducted in a mature evergreen forest near Santarém, Brazil. The exclusion manipulation lowered annual N2O emissions in four out of five treatment years (a natural drought year being the exception), and then recovered during the first year after the drought treatment stopped. Similarly, consumption of atmospheric CH4 increased under drought treatment, except during a natural drought year, and it also recovered to pretreatment values during the first year that natural throughfall was permitted back on the plot. No treatment effect was detected for NO emissions during the first 3 treatment years, but NO emissions increased in the fourth year under the extremely dry conditions of the exclusion plot during a natural drought. Surprisingly, there was no treatment effect on soil CO2 efflux in any year. The drought treatment provoked significant tree mortality and reduced the allocation of C to stems, but allocation of C to foliage and roots were less affected. Taken together, these results suggest that the dominant effect of throughfall exclusion on soil processes during this 6-year period was on soil aeration conditions that transiently affected CH4, N2O, and NO production and consumption.