A method of operating a wind turbine having at least one rotor blade and an active flow control (AFC) system is provided. The at least one rotor blade has at least one aperture defined through a surface thereof, and the AFC system is configured to modify aerodynamic properties of the rotor blade by ejecting gas through the aperture. The method includes operating the wind turbine in a normal mode, determining whether an estimated insect density value surrounding the wind turbine is above an insect density threshold value based on a measured environmental condition, and changing a mode of the wind turbine from the normal mode to a cleaning mode different than the normal mode based on the estimated insect density value. The cleaning mode includes adjusting at least one operation parameter of the wind turbine based on the estimated insect density value such that fouling of the aperture is reduced.