An experiment was performed on boundary layer suction, on a flat plate in a low turbulence wind-tunnel. This work focused on the process of ‘over-suction’ where at high suction rates, local flow structures around the suction perforations precipitate a premature laminar-to-turbulent transition instead of delaying the process. The historical ‘over-suction’ mechanism associated with widely spaced perforations, i.e. sufficiently widely spaced for local flow structures to act in isolation was studied. This high-frequency (St ~ 30–90) mechanism was identified and found to dominate in the absence of a pre-established transition front; however, where the natural transition front is pre-located close to the suction array (in the absence of suction): it was found that the dominant mechanism of ‘over-suction’ changed. The dominant modes during this new process was found to be at low frequency (St ~ 0.3–6). These low frequency modes appeared to be associated with inflectional instability, being sensitive to inflection points in wall normal profile of the span-wise mean velocity. The implications of this work is that the natural transition front location will need to be accounted for in the avoidance of ‘over-suction’ in the design of boundary layer suction systems.