At present, the problem of water ecological environment damage is becoming more and more severe. The compensation consultation for the water ecological environment damage is a system innovation of protecting the ecological environment. It conforms to the needs of ecological and social development, and has three functions: balancing the ecological and other interests, improving the efficiency of ecological damage relief and maintaining the ecological order. However, the specific implementation of this system may face the confusion of the subject status of consultation rights, the poor connection mechanism between consultation and litigation, and the imbalance between environmental ecological interests and other social public interests. Therefore, in view of the particularity of the water ecological environment, based on the improvement of the system of substantive law and procedural law, it is imperative to carry out the system reform of consultation on compensation for the water ecological environment damage.