A wind turbine system comprising a nacelle mounted on a tower, a rotor having a plurality of blades and a boundary layer control system configured to control airflow through blade surface openings in each of the blades. The wind turbine system includes a control system configured to perform at least one of the following: to monitor an operational speed parameter of the wind turbine, and to activate the boundary layer control system if it is determined that the 1 operational speed parameter exceeds a predetermined speed parameter threshold; to monitor tower motion and to activate the boundary layer control system based on a determination of excessive tower motion; to monitor for a wind turbine shutdown condition, and to activate the boundary layer control system if it is determined that a wind turbine shutdown condition has been identified; and to monitor the aerodynamic loads on the blades, and to activate the boundary layer control system also based on a determination of excessive blade loads. The system thereby provides an approach to activating and deactivating the boundary layer control system to reduce operational risk to the wind turbine.