The plasma treatment of polymer surfaces is routinely used to enhance surface properties prior to adhesive bonding or biomolecule interaction. This study investigates the influence of plasma treatment conditions on the surface activation of polyethylene terephthalate (PET) using the SurFx Atomflo (TM) 400L plasma source. In this study the effect of applied plasma power, processing speed, gas composition and plasma applicator nozzle to substrate distance were examined. The level of polymer surface activation was evaluated based on changes to the water contact angle (WCA) of PET samples after plasma treatment. PET surface properties were also monitored using surface energy and X-ray photoelectron spectroscopy (XPS) analysis. The heating effect of the plasma was monitored using thermal imaging and optical emission spectroscopy (OES) techniques. OES was also used as a diagnostic tool to monitor the change in atomic and molecular species intensity with changes in experimental conditions in both time and space. XPS analysis of the PET samples treated at different plasma powers indicated that increased oxygen content on samples surfaces accounted for the decreases observed in WCAs. For the first time a direct correlation was obtained between polymer WCA changes and the OES measurement of the atomic hydrogen Balmer H-alpha and molecular OH line emission intensities.