Water scarcity will increase due to climate change, especially in basins that are currently highly stressed. The Mediterranean area is one of the most vulnerable areas in the world, with a predicted natural water resource reduction of 20% to 35% at the end of the century, due to temperature increases and a 10–20% precipitation reduction. Water scarcity indices, including gross abstraction, net abstraction, and consideration of environmental requirements, can be efficiently used to analyse the effects of climate change in water resource systems and determine the main measures to adapt these systems to climate change. Increasing the reclaimed water use, seawater desalination, irrigation efficiency, and interconnecting water resource systems are the main measures to adapt basins under water stress and reduce their vulnerability to climate change. In the Júcar River Basin District (JRBD), with a 20% reduction in natural water resources, the main measures are: increasing the reclaimed water use in agriculture from 20% to 50% (91 hm3/year to 230 hm3/year), increasing seawater desalination from 30 to 55 hm3/year, increasing irrigation efficiency from 54% to 80%, and finally, fully developing the current water interconnections between water resource systems. In highly stressed basins, moving water from downstream to upstream using energy supplied by photovoltaic systems can help adapt river basins to climate change.