In the present study, effective hydrodynamic pressure modeling methods for three-dimensional earthquake safety analysis of a dam intake tower structure are investigated. Time history analysis results using the Westergaard added mass and Chopra added mass methods are compared with the one by the CASI (Coupled Acoustic Structural Interaction) method, which is accepted as giving almost exact solutions, to evaluate the difference in displacement response, stress and dynamic eccentricity. The 3D time history analysis of a realistic intake tower, which has the standard geometry widely used in Korea, shows that the Chopra added mass method gives similar results in displacement and stress and less conservative results in dynamic eccentricity to CASI ones, while the Westergaard added mass yields much more conservative results in all measures. This study suggests to use the CASI method directly for three-dimensional earthquake safety analysis of a dam intake tower, if computationally possible.