Rooting depth is a strong determinant of many hydrological and biogeochemical processes. This chapter examines the consequences of root distributions, particularly deep roots, for carbon and water fluxes. Although more than 90% of root biomass is usually in the top meter of soil, there are dozens of plant species that grow roots more than 10 m deep and at least half a dozen with roots below 50 m. The exchange of deep- and shallow-rooted species can alter the lateral movement of water, the depth of the water table, and conditions of salinization and waterlogging. In the Amazon, ignoring roots below 2 m would have underestimated evapotranspiration by up to 60%, and ignoring the soil below 1 m would have omitted a carbon pool larger than either the vegetation or the top meter of soil. In forests of the Carolina Piedmont, at least 8 m of the soil profile bears the biogeochemical imprint of biological activity. Correlational evidence there and in desert systems indicates that rooting depth may control the distribution of microbes and soil fauna to at least 12 m depth. To integrate the effects of deep soil processes (and to predict when the deep soil may be unimportant), global databases of depth to bedrock, soil texture, water holding capacity, waterlogged areas, and maximum rooting depth would be useful for ecosystem and global models and for testing hypotheses. The chapter highlights numerous unanswered questions, including whether deep roots increase ecosystem productivity through hydraulic lift and enhanced deep percolation of water, and how rooting depth affects whether an ecosystem is relatively open or closed.