The shortage and uneven spatial and temporal distribution of water resources has seriously restricted the sustainable development of regional society and economy. In this study, a metabolic theory for regional water resources was proposed by introducing the biological metabolism concept into the carrying capacity of regional water resources. In the organic metabolic process of water resources, the socio-economic system consumes water resources, while products, services and pollutants, etc. are output. Furthermore, an evaluation index system which takes into the characteristics of the regional water resources, the socio-economic system and the sustainable development principle was established based on the proposed theory. The theory was then applied to a case study to prove its availability. Further, suggestions aiming at improving the regional water carrying capacity were given on the basis of a comprehensive analysis of the current water resources situation.