Treatment of fluorinated ethylene propylene (FEP) and polytetrafluoroethylene (PTFE) by plasmas established in water vapour or ammonia gas enabled the rapid and facile modification of their surface chemistries. Under comparable plasma conditions, ammonia plasma exposures produced considerably lower air/water contact angles than water vapour plasmas. On storage of samples in air at ambient temperature, contact angles increased markedly within a few days on ammonia plasma-treated samples but remained constant over many weeks on water plasma-treated surfaces. Angle-dependent X-ray photoelectron spectroscopy (XPS) demonstrated a very low depth of modification in the case of ammonia plasma exposure, whereas the oxygen content of water plasma-treated samples was invariant with depth within the XPS analysis region. The long-term stability of water plasma-treated fluorocarbon polymer surfaces is believed to be due to this deep modification which prevents polymer chain reorientation, whereas the shallow modification in ammonia plasmas allows the rapid partial burial of the newly attached chemical groups inside the polymer. When ammonia plasma-treated samples stored in air were immersed in water, the contact angles remained constant, suggesting that the buried groups could not resurface. Contact angle measurements provided a simple and sensitive method for studying the time-dependent reduction in plasma treatment effects and the segmental mobility of modified fluorocarbon polymer surfaces; very shallow reorientation movements can be detected.