Exposure to hyperoxic conditions can induce pulmonary oxygen toxicity (POT). Divers of the Special Operations Forces (SOF) use oxygen rebreather systems during dives, and therefore are frequently exposed to hyperoxic conditions. Few studies have reported on POT in this population. This study reports on long-term pulmonary function tests (PFTs) and diffusing capacity in SOF divers to test the hypothesis that these measures of pulmonary function do not change clinically significantly during their career. The Royal Netherlands Navy performs yearly medical assessments of its military divers. All PFT and diffusing capacity data of SOF divers between the years 2000 and 2020 were analyzed using generalized estimating equations. The study included 257 SOF divers (median age, 27; interquartile range, 24–32), with 1612 dive medical assessments and a maximum follow-up time of 18.8 years. Alveolar volume (VA) and the diffusing capacity of carbon monoxide (TLCO) were significantly lower at baseline in smokers. Although these parameters were within the normal range, they declined over time and were significantly associated with age and years of diving. Smoking additionally affected TLCO and the transfer coefficient for carbon monoxide (KCO). TLCO and KCO were reduced by years of diving with oxygen rebreathers, albeit over clinically insignificant ranges, but smoking increased these changes by factors of 10 and 15, respectively.