Following rapid infrastructure development and industrialization, the problems of water pollution and water shortage have become more severe. Whether there is safe drinking water in cities has attracted wide attention. The ecological risk management of drinking water project is an important means of ensuring the safety of a drinking water source. Based on ecological risk assessment and management theories, this paper establishes an ecological risk management model and assessment system with the aim of providing theoretical guidance and scientific basis for formulating a policy on the safety and protection of drinking water sources in a city. Kunming is one of the cities plagued by severe water shortage in China. Its ecological risk management of drinking water has attracted the attention of both the local government and the public. Using Kunming as the case study, this paper conducts a comparative analysis and assessment on three major reservoirs that face ecological risks. It highlights the existing problems and gives helpful suggestions.