Structural Health Monitoring of strategical transportation infrastructures is becoming a pressing concern due to their ageing and degradation, particularly regarding the safety assessment of bridges and viaducts that are part of the modern railway network, especially for high-speed train operations. In the context of assessing the dynamic behaviour of common short-to-medium span railway bridge typologies under operational conditions, this work presents the results from the experimental dynamic identification of two prestressed reinforced concrete (P.R.C.) railway bridges. The experimental accelerometric data were acquired in operating conditions, hence, recording both ambient vibrations and train passages. In particular, Ambient Vibration Tests (AVT) were performed through a novel Automated Operational Modal Analysis (AOMA) algorithm to identify the modal parameters (natural frequencies, damping ratios, and mode shapes), here intended to serve as damage-sensitive features. The results are compared to those obtained using state-of-the-art commercial software (ARTeMIS).