Efficient modeling on uncertain information plays an important role in estimating the risk of contaminant intrusion in water distribution networks. Dempster-Shafer evidence theory is one of the most commonly used methods. However, the Dempster-Shafer evidence theory has some hypotheses including the exclusive property of the elements in the frame of discernment, which may not be consistent with the real world. In this paper, based on a more effective representation of uncertainty, called D numbers, a new method that allows the elements in the frame of discernment to be non-exclusive is proposed. To demonstrate the efficiency of the proposed method, we apply it to the water distribution networks to estimate the risk of contaminant intrusion.