During Earthquake motion, the responses of substructure and superstructure depend on the foundation soil/rock media and vice versa. Therefore, it is required to analyze the structures or foundation systems considering Soil-Structure Interaction behavior. In this study, Larji barrage (situated in Himachal Pradesh, India) is taken for analysis. Obtaining an analytical solution is a cumbersome job, hence a suitable numerical technique Finite Element Method is implemented here. A 3-Dimensional Finite Element model has been developed for Barrage and its components considering bay 3–4 and interacting soil and rock domain. Modal Analysis of Barrage has been performed taking two cases: Only barrage, and barrage interacting with soil or rock media. The natural frequencies and corresponding mode shapes are determined in each case. Parametric studies have been carried out depending upon geotechnical parameters. It is observed that modulus of elasticity has significant effects on modal responses whereas Poisson’s ratio has no significant involvement. Modal responses have been also compared for actual site condition (soil and rock strata both) and assumed condition (replacement of rock with soil), actual condition provides higher natural frequencies than assumed one.