Water is essential for the world’s food supply, for energy production, including bioenergy and hydroelectric power, and for power system cooling. Water is already scarce in many regions and could present a critical constraint as society attempts simultaneously to mitigate climate forcing and adapt to climate change, and to provide food for an increasing population. We use the Global Change Assessment Model (GCAM), where interactions between population, economic growth, energy, land and water resources interact simultaneously in a dynamically evolving system, to investigate how water scarcity affects energy and land use decisions as well as mitigation policies. In GCAM, competing claims on water resources from all claimants—energy, land, and economy—are reconciled with water resource availability—from renewable water, non-renewable groundwater sources and desalinated water—across 235 major river basins. Limits to hydrologic systems have significant effects on energy and land use induced emissions via constraints on decisions of their use. We explore these effects and how they evolve under climate change mitigation policies, which can significantly alter land use patterns, both by limiting land use change emissions and by increasing bioenergy production. The study also explores the mitigation scenarios in the context of the shared socioeconomic pathways (SSPs). We find that previous estimates of global water withdrawal projections are overestimated, as our simulations show that it is more economical in some basins to alter agricultural and energy activities rather than utilize non-renewable groundwater or desalinated water. This study highlights the fact that water is a binding factor in agriculture, energy and land use decisions in integrated assessment models (IAMs), and stresses the crucial role of water in regulating agricultural commodities trade and land-use and energy decisions.