With the development of human society and economy and its gradual strengthening of interference to the water resources system, the importance of water resources protection is becoming increasingly prominent, its definition and connotation are constantly evolving, showing the characteristics of watershedization, systemization, and ecologicalization. Based on the quantitative evaluation of human activities interference with China water resources in terms of water consumption, water pollution discharge, water space occupancy, and water channel barriers, which result in the reduction of aquatic biodiversity, this paper inherits and develops the traditional water resources protection connotation, proposes a new concept of river basin water resources protection in the new era with “quantity-quality-domain-connectivity-biology” coordinated protection and restoration as core, clarifies the framework, key tasks and evaluation indicators of river basin water resources protection, and proposes the key technologies of river basin water resources protection that need to be studied in the future compared with the existing technical system. The protection of river basin water resources is an upgrade of traditional water resources protection, which has important promotion significance for the reform and development of water conservancy in the new era and the construction of a beautiful China.