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Abstract: The landscape of central Amazonia is composed of plateaus and valleys. Previous observations have shown preferential pooling of CO2 in the valleys, suggesting that the change in CO2 storage in the canopy air space (S) will be spatially variable at the scale of the topography. This may affect the interpretation of the net ecosystem CO2 exchange (NEE) rates measured on the plateaus if they have used one single atmospheric CO2 concentration ([CO2]) vertical profile measurement system. We have measured the diel, spatial and seasonal variation of S along the topography by using a set of automated [CO2] vertical profile measurement systems. In addition, NEE, the above-canopy turbulent exchange of CO2 (F c ) and meteorological variables were also measured on a micrometeorological tower located on the plateau. The nocturnal accumulation of CO2 was larger on the slopes and in the valleys than on the plateau and was larger in the dry period than in the wet period. In addition, the release of this CO2 occurred later in the day on the slopes and in the valleys than on the plateau. Differences in the flow regime above the canopy along the topographical gradient, lateral drainage of respired CO2 downslope, and temporal, spatial, and seasonal variation of soil CO2 efflux (R soil) are thought to have contributed to this. These conditions cause S to be higher in magnitude on the slopes and in the valleys than on the plateau during midmorning hours. We demonstrate that there is a larger underestimation of R eco by nighttime eddy covariance (EC) measurements in the dry period than in the wet period. In addition, R eco – as derived from measurements only on the plateau (F c + S P) – does not agree with that derived by an independent method. Yet S fluxes peaked at about 18:00–20:00 on the slopes and in the valleys, following a continuous decrease after this period until reaching a minimum just after dawn. NEE derived from F c measured on the plateau and S measured on the plateau, slope and valley increased the estimates of R eco on the plateau by about 30% and 70% in the wet and dry periods, respectively. Particularly for flux-tower sites over complex terrain, we recommend measuring the spatial variability of CO2 at, at least two, more points along the topography to determine to what extent horizontal gradients and storage changes may contribute to tower fluxes. Finally, for sites that present topographical characteristics similar to that described in this study, care must be taken with the use of single in-canopy profiles of [CO2] to correct EC fluxes. [Copyright &y& Elsevier]