High ground-level ozone concentrations are typical of Mediterranean climates. Plant exposure to this oxidant is known to reduce carbon assimilation. Ozone damage has been traditionally measured through manipulative experiments that do not consider long-term exposure and propagate large uncertainty by up-scaling leaf-level observations to ecosystem-level interpretations. We analyzed long-term continuous measurements (>9 site-years at 30 min resolution) of environmental and eco-physiological parameters at three Mediterranean ecosystems: (i) forest site dominated by Pinus ponderosa in the Sierra Mountains in California, USA; (ii) forest site composed of a mixture of Quercus spp. and P. pinea in the Tyrrhenian sea coast near Rome, Italy; and (iii) orchard site of Citrus sinensis cultivated in the California Central Valley, USA. We hypothesized that higher levels of ozone concentration in the atmosphere result in a decrease in carbon assimilation by trees under field conditions. This hypothesis was tested using time series analysis such as wavelet coherence and spectral Granger causality, and complemented with multivariate linear and nonlinear statistical analyses. We found that reduction in carbon assimilation was more related to stomatal ozone deposition than to ozone concentration. The negative effects of ozone occurred within a day of exposure/uptake. Decoupling between carbon assimilation and stomatal aperture increased with the amount of ozone pollution. Up to 12–19% of the carbon assimilation reduction in P. ponderosa and in the Citrus plantation was explained by higher stomatal ozone deposition. In contrast, the Italian site did not show reductions in gross primary productivity either by ozone concentration or stomatal ozone deposition, mainly due to the lower ozone concentrations in the periurban site over the shorter period of investigation. These results highlight the importance of plant adaptation/sensitivity under field conditions, and the importance of continuous long-term measurements to explain ozone damage to real-world forests and calculate metrics for ozone-risk assessment.