This paper presents the first application of the Laser Doppler Vibrometer (LDV) in non-stationary conditions within a hydropower plant powerhouse. The aim of this research is to develop a methodology to include non-contact vibration monitoring as part of structural health monitoring of concrete dams. We have performed in-situ structural vibration measurements on the run-of-the-river Brežice dam in Slovenia during the start-up tests and regular operation. In recent decades, the rapid development of laser measurement technology has provided powerful methods for a variety of measuring tasks. Despite these recent developments, the use of lasers for measuring has been limited to sites provided with stationary conditions. This paper explains the elimination of pseudo-vibration and measurement noise inherent in the non-stationary conditions of the site. Upon removal of the noise, fatigue of the different structural elements of the powerhouse could be identified if significant changes over time are observed in the eigenfrequencies. The use of laser technology is to complement the regular monitoring activities on large dams, since observation and analysis of integrity parameters provide indispensable information for decision making and maintaining good structural health of ageing dams.