The carbon and water cycles for a southwestern Amazonian forest site were investigated using the longest time series of fluxes of CO2 and water vapor ever reported for this site. The period from 2004 to 2010 included two severe droughts (2005 and 2010) and a flooding year (2009). The effects of such climate extremes were detected in annual sums of fluxes as well as in other components of the carbon and water cycles, such as gross primary production and water use efficiency. Gap-filling and flux-partitioning were applied in order to fill gaps due to missing data, and errors analysis made it possible to infer the uncertainty on the carbon balance. Overall, the site was found to have a net carbon uptake of ≈5 t C ha(-1) year(-1), but the effects of the drought of 2005 were still noticed in 2006, when the climate disturbance caused the site to become a net source of carbon to the atmosphere. Different regions of the Amazon forest might respond differently to climate extremes due to differences in dry season length, annual precipitation, species compositions, albedo and soil type. Longer time series of fluxes measured over several locations are required to better characterize the effects of climate anomalies on the carbon and water balances for the whole Amazon region. Such valuable datasets can also be used to calibrate biogeochemical models and infer on future scenarios of the Amazon forest carbon balance under the influence of climate change.