We simulated the variability in natural ecosystem carbon storage under historical conditions (1895-1994) in six regions of the conterminous USA as delineated for the USGCRP National Assessment (2001). The largest simulated variations in carbon fluxes occurred in the Midwest, where large fire events (1937, 1988) decreased vegetation biomass and soil carbon pools. The Southeast showed decadal-type trends and alternated between a carbon source (1920s, 1940s, 1970s) and a sink (1910s, 1930s, 1950s) in response to climate variations. The drought of the 1930s was most obvious in the creation of a large carbon source in the Midwest and the Great Plains, depleting soil carbon reserves. The Northeast shows the smallest amplitudes in the variation of its carbon stocks. Western regions release large annual carbon fluxes from their naturally fire-prone grassland- and shrubland dominated areas, which respond quickly to chronic fire disturbance, thus reducing temporal variations in carbon stocks. However, their carbon dynamics reflect the impacts of prolonged drought periods as well as regional increases in rainfall from ocean-atmosphere climate regime shifts, most evident in the 1970s. Projections into the future by using the warm CGCM1 climate scenario show the Northeast becoming mostly a carbon source, the Southeast becoming the largest carbon source in the 21st century, and the two western-most regions becoming carbon sinks in the second half of the 21st century. Similar if more moderate trends are observed by using the more moderately warm HADCM2SUL scenario.