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 is obtained, but it has a weak point that virtual kinematic viscosity coefficient ν_w must be used in the shallow water to express the phenomena. In this paper, to express the phenomena in the shallow water, modulus of velocity distribution β_w is introduced as a new parameter, and the damping matrix is redefined by using β_w. We can regard β_w as the parameter to estimate the influence of the water depth upon the damping matrix, because it is proportional constant on the damping matrix. If β_w is given according to the water depth, not only the frequency response curve in the shallow water can be reproduced but also the frequency response curve in the deep water can be estimated by using the transfer function in the shallow water. Therefore it is necessary to develop a method to experimentally obtain β_w. Hence the authors developed the method by using the partial differential iteration method which is one of the curve fit algorithm. The formulation and the results are described.