Rooting depth is an ecosystem trait that determines the extent of soil development and carbon (C) and water cycling. Recent hypotheses propose that human-induced changes to Earth’s biogeochemical cycles propagate deeply due to rooting depth changes from agricultural and climate-induced land cover changes. Yet, the lack of a global-scale quantification of rooting depth responses to human activity limits knowledge of hydrosphere-atmosphere-lithosphere feedbacks in the Anthropocene. Here we use land cover datasets to demonstrate that root depth distributions are changing globally as a consequence of agricultural expansion truncating depths above which 99% of root biomass occurs (D99) by ~60 cm, and woody encroachment linked to anthropogenic climate change extending D99 in other regions by ~38 cm. The net result of these two opposing drivers is a global reduction of D99 by 5%, or ~8 cm, representing a loss of ~11,600 km3 of rooted volume. Projected land cover scenarios in 2100 suggest additional future D99 shallowing of up to 30 cm, generating further losses of rooted volume of ~43,500 km3, values exceeding root losses experienced to date and suggesting that the pace of root shallowing will quicken in the coming century. Losses of Earth’s deepest roots — soil-forming agents — suggest unanticipated changes in fluxes of water, solutes, and C. Two important messages emerge from our analyses: dynamic, human-modified root distributions should be incorporated into earth systems models, and a significant gap in deep root research inhibits accurate projections of future root distributions and their biogeochemical consequences.