Huaihe River basin is one of the key areas for the water environment control. Due to its complicated water situation, water pollution is easy to happen. This paper considers the situation of emergent water pollution and how to schedule the ecological water in the dams and reservoirs to control the pollution in the shortest time. Dam scheduling problem is the combinatorial optimization problem, and the efficiency of scheduling is the objective function. The constraints include water storage capacity, concentration of water and dam distance. In this paper, the artificial fish swarm algorithm (AFSA) is applied to water pollution control requirements, which is adopted and satisfied. AFSA has the advantage of fast track change and jumping out of local extremum, and can avoid possible premature problems at initial stage. Experimental results show that the water ecological scheduling method based on AFSA performs accurately and efficiently in dealing with such problems. It can find near optimal solutions within fewer iterations, and the results have better feasibility and referential.