Niche partitioning of resources by plants is believed to be a fundamental aspect of plant coexistence and biogeochemical cycles; however, measurements of the timing and location of resource use are often lacking because of the difficulties of belowground research. To measure niche partitioning of soil water by grasses, planted saplings, and trees in a mesic savanna (Kruger National Park, South Africa), we injected deuterium oxide into 102,000 points in 15, 154-m2 plots randomly assigned to one of five depths (0–120 cm) and one of three time periods during the 2008/2009 growing season. Grasses, saplings and trees all demonstrated an exponential decline in water uptake early in the season when resources were abundant. Later in the season, when resources were scarce, grasses continued to extract the most water from the shallowest soil depths (5 cm), but saplings and trees shifted water uptake to deeper depths (30–60 cm). Saplings, in particular, rapidly established roots to at least 1 m and used these deep roots to a greater extent than grasses or trees. Helping to resolve contradictory observations of the relative importance of deep and shallow roots, our results showed that grasses, saplings and trees all extract the most water from shallow soils when it is available but that woody plants can rapidly shift water uptake to deeper soils when resources are scarce. Results highlight the importance of temporal changes in water uptake and the problems with inferring spatial and temporal partitioning of soil water uptake from root biomass measurements alone.