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 climates. Here we report results of a large-scale (1 ha) throughfall exclusion experiment conducted in a mature evergreen forest near Santarém, Brazil. The exclusion manipulation lowered annual N2O emissions by >40% and increased rates of consumption of atmospheric CH4 by a factor of >4. No treatment effect has yet been detected for NO and CO2 fluxes. The responses of these microbial processes after three rainy seasons of the exclusion treatment are characteristic of a direct effect of soil aeration on denitrification, methanogenesis, and methanotrophy. An anticipated second phase response, in which drought-induced plant mortality is followed by increased mineralization of C and N substrates from dead fine roots and by increased foraging of termites on dead coarse roots, has not yet been detected. Analyses of depth profiles of N2O and CO2 concentrations with a diffusivity model revealed that the top 25 cm soil is the site of most of the wet season production of N2O, whereas significant CO2 production occurs down to 100 cm in both seasons, and small production of CO2 occurs to at least 1100 cm depth. The diffusivity-based estimates of CO2 production as a function of depth were strongly correlated with fine root biomass, indicating that trends in belowground C allocation may be inferred from monitoring and modeling profiles of H2O and CO2.