The degree to which primary production, soil carbon, and trace gas fluxes in tropical forests of the Amazon are limited by moisture availability and other environmental factors was examined using an ecosystem modelling application for the country of Brazil. A regional geographical information system (GIS) serves as the data source of climate drivers, satellite images, land cover, and soil properties for input to the NASA Ames-CASA (Carnegie-Ames-Stanford Approach) model over a 8-km grid resolution. Simulation results lead us to hypothesize that net primary production (NPP) is limited by cloud interception of solar radiation over the humid north-western portion of the region. Peak annual rates for NPP of nearly 1.4 kg C m–2 year–1 are localized in the seasonally dry eastern Amazon in areas that we assume are primarily deep-rooted evergreen forest cover. Regional effects of forest conversion on NPP and soil carbon content are indicated in the model results, especially in seasonally dry areas. Comparison of model flux predictions along selected eco-climatic transects reveal moisture, soil, and land use controls on gradients of ecosystem production and soil trace gas emissions (CO2, N2O, and NO). These results are used to formulate a series of research hypotheses for testing in the next phase of regional modelling, which includes recalibration of the light-use efficiency term in NASA-CASA using field measurements of NPP, and refinements of vegetation index and soil property (texture and potential rooting depth) maps for the region.