A numerical method for the transmission loss prediction of the water muffler has been provided according to the measuring process of the two-load method. The commonly used acoustic loads can be applied in the proposed method. The accuracy of the proposed method has been proved by comparing the calculated transmission loss with that from the traditional direct predicting method. And then the proposed method is used to discuss effects of test bench on transmission loss measurement. The predicted transmission loss curves are consistent reasonably based on different test models. The location of monitors relative to the muffler inlet and outlet has little influence on the result. But the distance between the two monitors upstream or downstream should be controlled within a certain range based on the concerning frequency band and the main pipe diameter. It is found that modes of the coupled system consisting of the test pipes and the water cause extra peaks on the transmission loss curve. The influence can be reduced by arranging appropriate fixed points. The proposed method can be used to to explain the reasonability and validity of the test bench design.