An active flow control system for manipulating a boundary layer of air across a wind turbine rotor blade. The wind turbine rotor blade has at least one sidewall defining a cavity therein. The sidewall extends between a leading edge and an axially spaced trailing edge. The active flow control system includes an air discharge assembly that is coupled to the sidewall. The air discharge assembly is configured to selectively discharge air from within the wind turbine rotor blade into the boundary layer. An air suction assembly is coupled to the sidewall and to the air discharge assembly. The air suction assembly is configured to channel air from the boundary layer to the air discharge assembly.