Currently, water demands are increasing notoriously, spreading the pressure on available water resources around the world in both quantity and quality. Similarly, the expected reduction of natural water inputs, due to climate change, depicts a new level of uncertainty. Specifically, Southeast Spain presents water scarcity due to its aridity—irregular and scarce precipitation and high evapotranspiration rates—combined with the competition between several water demands: environment, agricultural dynamics, urban-tourist activities, and industry. The study area of this work is the most relevant functional urban area of Alicante province (SE Spain), where the administration of water management is carried out by a range of authorities at different levels as the consequence of a complex historical development of water governance schemes: at the national, regional, and local levels. This study analyzes 21 municipalities and proposes a conceptual model which was developed by including different origins of water inputs—surface resources, groundwater, desalination, wastewater reuse, or interbasin transfers—and water demands with information obtained from 16 different sources. Our main results denote a relevant water deficit of 72.6 hm3/year even when one of the greatest rates of desalinated water and reused wastewater in Europe are identified here. This negative balance entails restrictions in urban development and agricultural growth. Thus, presented results are noteworthy for the water policy makers and planning authorities, by balancing the demand for water among various end users and providing a way for understanding water distribution in a context of scarcity and increasing demand, which will become one of the most challenging tasks in the 21st century.