Castelporziano Estate is a coastal forest 25 km from downtown Rome. It is an ideal site to study interactions between Mediterranean forest ecosystems and a polluted atmosphere. Two eddy covariance systems were used to simultaneously measure water vapour and ozone fluxes above and below a canopy of Holm Oak (Quercus ilex). Additional measurements of environmental parameters allowed to calculate stomatal ozone fluxes in order to parameterize atmospheric models and new algorithms for discriminating ozone deposition into its three more significant sinks: soil, stomata, and cuticles. Results showed that stomata explained almost the totality of ozone fluxes during the winter season, and <60% during the warm seasons under condition of drought stress. Soils removed up to 30% of ozone, suggesting the importance of this sink in this forest ecosystem. This study spanning all seasons over a 2-year period advanced our understanding about the contribution of a representative Mediterranean Oak forest to biosphere–atmosphere exchange.