This paper proposes a novel segmentation approach that extends frequency domain operational modal analysis methods to analyze structures dealing with non-uniform, non-stationary, and mixed high-energy harmonic excitations with low signal-to-noise ratios. The paper first discusses the impact of excitations in a hydroelectric dam on the structural response and modal parameters. The method introduces three indicators for selecting the best segments to capture the structural modes. The proposed method is applied to the field-collected data from the long-term monitoring of the Mactaquac Dam intake structure. The Mactaquac Generating Station is the largest hydroelectric power plant in the Canadian Maritime Provinces. The presented study in this paper is part of the Mactaquac Life Achievement Project to ensure the station can operate to its intended 100-year lifespan.