An algorithm of operational modal analysis in time domain is presented for thediscrimination between structural modes, harmonic excitations and spurious modes. Aclassification factor is developed and based on the construction of the damped signal- to-noise ratio which separates the physical modes from the numerical ones. The harmonicexcitations are then recognized at very high power indexes and zero damping. Furthermore, after the modal discrimination, the harmonic spectrum and the estimated frequency responsefunction can be derived. The method can be updated in the time domain either by a shorttime sliding window or a recursive technique to provide the modal monitoring in bothstationary and non-stationary process. An industrial application on a hydro-electricalgenerator is discussed to identify the machine frequencies under operational workingconditions.