This paper is focused on the study of the dynamic behaviour of two large arch dams, and it presents some innovations for the improvement of Seismic and Structural Health Monitoring (SSHM) systems for dams. The work describes a methodology based on the integrated use of software for automatic monitoring data analysis and of computational 3D finite element (3DFE) models for dam dynamic behaviour simulation. The monitoring data analysis software was developed for automatic modal identification, in order to obtain natural frequencies and mode shapes, for automatic detection of vibrations induced by seismic events, to be distinguished from those caused by other operational sources, and for comparison between results retrieved from measured vibrations and numerical results from 3DFE modelling. The numerical simulations are carried out using a 3DFE program developed for dynamic analysis of dam-reservoir-foundation systems, based on a solid–fluid coupled formulation and considering the dam-water dynamic interaction, including calculation modules for complex modal analysis and for linear and non-linear seismic analysis. The case studies are two large arch dams that have been under continuous dynamic monitoring over the last ten years: Cabril dam (132 m high), the highest dam in Portugal, and Cahora Bassa dam (170 m high), in Mozambique, one of the highest dams in Africa. The SSHM systems installed in both dams have similar schemes and were designed to continuously record accelerations in several locations at the upper part of the dam body and near the dam-foundation interface, using uniaxial and triaxial accelerometers. The most significant experimental results from continuous dynamic monitoring are presented and compared with numerical results for both dams, with emphasis on the evolution of natural frequencies over time, including the vibration mode shapes for various water levels, and on the measured accelerations during low-intensity seismic events. Furthermore, the main results of non-linear seismic response simulations are provided, considering the effects due to joint movements and tensile and compressive concrete damage, aiming to assess the seismic performance of both dams based on the Endurance Time Analysis method.