Secretions that have accumulated at or near an airway of a subject as the subject is being mechanically ventilated are removed by suctioning. Before, during, and/or after the removal of the secretions, steps are taken to mitigated the impact of the suctioning used for secretion removal on the subject. As such, the timing of suction used to remove secretions may be influenced or controlled, ventilation of the subject during suction may be adjusted, ventilation of the subject prior to secretion removal may be adjusted to prepare the lungs of the subject for secretion removal, ventilation of the subject subsequent to suction for secretion removal may be adjusted, and/or other techniques for reducing the impact of suctioning for secretion removal on the subject may be implemented.