The outstanding obstacle to estimate vibration level is that the precise damping of fluid and structure can not be estimated because the mechanism of the damping has not been explicated. Recently, the damping matrix based on dissipation energy caused by fluid viscosity has been obtained, and the damping matrix is expressed more rationally by introducing modulus of velocity distribution β _w as a parameter to estimate the influence of the water depth. We developed a method to obtain β _w both in the shallow water and in the deep water, by using experimental data in the air. But it is generally impossible to make an experiment using a real ship in the air. In this paper, we propose a method to obtain β _w by using only data in different water depths. Concretely, authors incorporate reduced added matrices into transfer function by means of modal structural modification analysis, and formulate the partial differential iteration method by using the transfer function. The formulation and the results are described.