Experience of the past earthquakes indicates that topographic magnification and surroundings of structure contribute to the destruction of structures after the earthquake. In this article, the dynamic interaction formulation of structures is presented. The method is based on the boundary element method in frequency domain. In order to assess the accuracy and efficiency of the proposed formulations for the dynamic interaction of structures, several problems are considered. Also, the structural analysis of morning glory spillway of Barzu dam located in Shirvan was investigated. For this purpose, every domain placed around the structure was modeled and analyzed separately, and then a model incorporating all the domains was presented.For realistic analysis, the problems were modeled and analyzed three-dimensionally. In this study, the effects of parameters such as shape irregularities, mechanical properties of materials (density, Poisson coefficient, shear modulus), stimulation frequency, incident wave type (P, SH, SV), azimuth and angle of incident wave on dynamic analysis of mentioned structure were considered.The results show that the foundation flexibility causes stiffness reduction and thus reduction of frequency vibrational modes of the system. The fluid-structure interaction brings about a high change in seismic response of the system in a way that the values of the displacements increase at frequencies lower than the 1.5 times of the first vibration mode and decrease at higher frequencies. The fluid in contact with structure increases the effective mass and reduces vibration frequencies of the system.