Purpose <p>The dynamic analysis of arch dams under seismic loading remains a critical area of research, particularly concerning dam-water-foundation interactions and foundation flexibility effects. This study employs a rigorous transfer function-based frequency domain spectral analysis of the full 3D dam-water-foundation interaction problem under random excitation, focusing on foundation stiffness effects, addressing a relatively less explored area identified in the literature.</p> Methods <p>This study investigates the seismic response of the Morrow Point arch dam using a detailed 3D finite element model subjected to random ground motion, modeled via the power spectral density function (PSDF) of the Kern County earthquake. Absorbing boundary conditions at the foundation and the upstream end of the reservoir water were implemented to prevent wave reflections by applying viscous dashpots at the foundation’s boundary nodes (sides and bottom) and a non-reflecting planar surface at the reservoir’s upstream end.</p> Results <p>For displacement responses, the root mean square (RMS) values obtained from spectral analysis and time history analysis differed by up to 10%, while the absolute mean peak values exhibited a maximum variation of 20%. For stress responses, these discrepancies were 12% for RMS values and 20% for absolute mean peak values across all foundation flexibility cases examined.</p> Conclusion <p>Key findings reveal that foundation stiffness significantly influences dynamic behavior; displacements and stresses at the center of the dam crest amplify with increasing foundation stiffness, whereas responses of the crest near the side support exhibit an inverse trend. Stress distribution analysis indicates that arch stresses dominate at the crest, while cantilever stresses prevail at the base. The PSDF responses align closely with transfer functions, suggesting resonating condition overriding pseudo-static condition.</p>