The continuous operation and structural integrity of wind turbines are critical for efficient energy production. Monitoring the dynamic behavior of wind turbines under operational regime presents significant challenges due to varying environmental and operational conditions. In the field of structural monitoring, Operational Modal Analysis (OMA) is a powerful tool for characterizing the dynamic behavior of operating systems through a set of modal parameters, without requiring controlled excitations. However, applying OMA to wind turbines introduces complexities such as dealing with the different dynamic behavior of these structures for different operational regimes of energy production, and tracking the resonance modes of wind turbines across the ever-changing rotational speeds across time. This work provides an in-depth discussion of the challenges in monitoring wind turbines, by discussing developed applications of Automated Operational Modal Analysis (AOMA) for the monitoring of a 2.0 MW wind turbine. This procedure includes three main steps: Modal Parameter Estimation (MPE), Automated Modal Parameter Selection (AMPS) and modal tracking. The obtained results and challenges identified for each of the steps is discussed in this paper.