The Amazon basin contains some of the most productive ecosystems on the planet, yet we have little understanding of the long-term behavior. By examining historical climate records over the Amazon, we identify several modes of climatic variability-including previously undocumented long-term modes. Furthermore, using a process-based ecosystem model, we show that these variations in climate generate variations in terrestrial carbon fluxes on short (3--4 year), intermediate (8--9 year), and long (24--28 year) time scales. The long-term cycles in terrestrial carbon balance have not been previously suggested. Finally, we find that time-lags between productivity and decomposition enhance the short-term variations in net carbon balance, while slightly dampening the long-term variations. Given the worldwide attention on terrestrial carbon cycling, and the potential for carbon sinks, we suggest that an improved understanding of long-term climatic and ecosystem processes is crucial. Other regions should be examined for potential long-term carbon cycle variations.