Flux measurements of carbon dioxide and water vapor above tropical rain forests are often difficult to interpret because the terrain is usually complex. This complexity induces heterogeneity in the surface but also affects lateral movement of carbon dioxide (CO2) not readily detected by the eddy covariance systems. This study describes such variability using measurements of CO2 along vertical profiles and along a toposequence in a tropical rain forest near Manaus, Brazil. Seasonal and diurnal variation was recorded, with atmospheric CO2 concentration maxima around dawn, generally higher CO2 build-up in the dry season and stronger daytime CO2 drawdown in the wet season. This variation was reflected all along the toposequence, but the slope and valley bottom accumulated clearly more CO2 than the plateaus, depending on atmospheric stability. Particularly during stable nights, accumulation was along lines of equal altitude, suggesting that large amounts of CO2 are stored in the valleys of the landscape. Flushing of this store only occurs during mid-morning, when stored CO2 may well be partly transported back to the plateaus. It is clear that, for proper interpretation of tower fluxes in such complex and actively respiring terrain, the horizontal variability of storage needs to be taken into account not only during the night but also during the mornings.