Drinking water safety is a safety issue that the whole society attaches great importance to currently. For sudden water pollution accidents, it is necessary to trace the water pollution source in real time to determine the pollution source’s characteristic information and provide technical support to emergency management departments for decision making. The problems of water pollution’s real-time traceability are as follows: non-uniqueness and dynamic real time of pollution sources. Aiming at these two difficulties, an intelligent traceability algorithm based on dynamic multi-mode optimization was designed and proposed in the work. As a multi-mode optimization problem, pollution traceability could have multiple similar optimal solutions. Firstly, the new algorithm divided the population reasonably through the optimal subpopulation division strategy, which made the nodes’ distribution in a single subpopulation more similar and conducive to local optimization. Then, a similar peak penalty strategy was used to eliminate similar solutions and reduce the non-unique solutions’ number, since real-time traceability required higher algorithm convergence than traditional offline traceability and dynamic problems with parameter changes, historical information preservation, and adaptive initialization strategies could make reasonable use of the algorithm’s historical knowledge to improve the population space and increase the population convergence rate when the problem changed. The experimental results showed the proposed new algorithm’s effectiveness in solving problems—accurately tracing the source of pollution, and obtain corresponding characteristic information in a short time.