DEFORESTATION and logging transform more forest in eastern and southern Amazonia than in any other region of the world1-3. This forest alteration affects regional hydrology4-11 and the global carbon cycle12-14, but current analyses of these effects neglect an important deep-soil link between the water and carbon cycles. Using rainfall data, satellite imagery and field studies, we estimate here that half of the closed forests of Brazilian Amazonia depend on deep root systems to maintain green canopies during the dry season. Evergreen forests in northeastern Pará state maintain evapotranspiration during five-month dry periods by absorbing water from the soil to depths of more than 8m. In contrast, although the degraded pastures of this region also contain deep-rooted woody plants, most pasture plants substantially reduce their leaf canopy in response to seasonal drought, thus reducing dry-season evapotranspiration and increasing potential subsurface runoff relative to the forests they replace. Deep roots that extract water also provide carbon to the soil. The forest soil below 1 m depth contains more carbon than does above-ground biomass, and as much as 15% of this deep-soil carbon turns over on annual or decadal timescales. Thus, forest alteration that affects depth distributions of carbon inputs from roots may also affect net carbon storage in the soil. © 2002 Nature Publishing Group.