The humid tropical zone is a major source area for N2O and NO emissions to the atmosphere. Local emission rates vary widely with local conditions, particularly land use practices which swiftly change with expanding settlement and changing market conditions. The combination of wide variation in emission rates and rapidly changing land use make regional estimation and future prediction of biogenic trace gas emission particularly difficult. This study estimates contemporary, historical, and future N2O and NO emissions from 0.5 million ha of northeastern Costa Rica, a well-documented region in the wet tropics undergoing rapid agricultural development. Estimates were derived by linking spatially distributed environmental data with an ecosystem simulation model in an ensemble estimation approach that incorporates the variance and covariance of spatially distributed driving variables. Results include measures of variance for regional emissions. The formation and aging of pastures from forest provided most of the past temporal change in N2O and NO flux in this region; future changes will be controlled by the degree of nitrogen fertilizer application and extent of intensively managed croplands.