In this study, the effect of hydrodynamic masses is investigated in the dynamic characteristics and earthquake response analyses of the submerged HANARO flow tubes. First, the consistent hydrodynamic masses of the surrounding water are obtained by finite element method. Then, modal analyses and response spectrum analyses are performed and verified by comparing the results with those measured from an experiment. Arbitrary cross-sections of submerged structures and boundary conditions of the surrounding fluid can be considered by using the general benefits of a finite element method comparing with the conventional analytical methods. Practical criteria based on parametric studies are proposed to evaluate the dynamic characteristics of HANARO flow tubes including the hydrodynamic masses.