Woody plants are encroaching into grasslands and savannas of the karst Edwards Plateau, but their impacts on climate and hydrology are unclear because of high variability in soil depth and uncertainties about the contribution of water in fractured limestone to the water available to trees. Water use is controlled by available energy (AE) and its partitioning between latent (λE) and sensible (H) heat fluxes. We hypothesized that the partitioning of AE depends on soil depth, with greater depth leading to more λE and less H. We compared energy fluxes of a deep soil savanna with ~50% woody cover dominated by Ashe juniper (Juniperus ashei) and a shallow soil woodland dominated by live oak (Quercus virginiana) and juniper over a 5-year period, which included periods of unusually high rainfall and severe drought. Although AE was 7% higher in the woodland, λE was about 2% higher at the savanna over the 5-year study. Site differences in evapotranspiration were maximal during dry periods between rainfall events, suggesting greater storage of water at the savanna site. During periods of high rainfall, the impact of water storage limitations was minimal, and site differences in evapotranspiration were controlled mainly by AE and its partitioning into H. Both sites were characterized by rapid reductions in λE and reciprocal increases in H during drying cycles following rainfall, indicating that neither of these ecosystems had access to easily utilized sources of deep water. Copyright © 2012 John Wiley & Sons, Ltd.