Background <p>Excessive vibration in vertical shaft hydropower units, primarily driven by rotor unbalance and bearing misalignment, poses significant risks to operational integrity and component longevity. Consequently, precise alignment and dynamic balancing are critical during commissioning and maintenance.</p> Methods <p>This study presents an integrated computational framework for the comprehensive analysis and correction of these anomalies. The methodology utilizes orthogonal displacement sensors positioned at five critical structural nodes: the thrust bearing, lower bracket, generator shaft flange, turbine shaft flange, and turbine guide bearing. Acquired data is processed via a custom-developed MATLAB algorithm to quantify runout and optimize shaft alignment. Furthermore, vibration characteristics are evaluated using Fast Fourier Transform (FFT) spectral analysis to identify synchronous deviations relative to ISO 20816-5 thresholds. distinct from traditional empirical methods, this research employs the vector-based Influence Coefficient Method (ICM) to calculate precise correction masses, thereby minimizing iterative adjustments.</p> Results <p>The proposed automated alignment and balancing protocol was experimentally validated on Unit 3 of the Dez Power Plant. Results demonstrate that the integrated approach successfully reduced vibration amplitudes to within permissible limits, ensuring dynamic stability and operational safety.</p> Conclusions <p>The integrated approach ensured vibration reduction, dynamic stability, and operational safety.</p>