Mediterranean forest ecosystems in Croatia are of very high significance because of ecological functions they provide. Due to the high sensitivity of this region to air pollutants present in the atmosphere, it is important to monitor the state of forest ecosystems and how they react to them. The aims of this research were to establish environmental monitoring in Mediterranean forest ecosystems, to determine the concentrations of atmospheric deposition and ground-level ozone, the physiological parameters of trees, to determine biochemical indicators of oxidative stress caused by abiotic sources of stress and finally to establish cause-and-effect relationships between physiological parameters of trees and atmospheric inputs. All measurements, sampling and analysis were done according to International co-operative programme on assessment and monitoring of air pollution effects on forests (ICP Forests) manuals. The highest amount of atmospheric deposition was in the holm oak forest. Nitrogen critical loads did not cross literature limit. Ozone on all four plots was found to be close to or reached 100 ppb. The lowest defoliation was determined on the holm oak plot with < 10% while on the other three it was > 40%, and the highest growth percentage was on Aleppo pine plot. The relationship between environmental variables and forest health indicators (defoliation and growth) was found that defoliation was significantly correlated with soil water content at different depths, while growth was correlated with solar radiation, moisture and with all ozone parameters. Using random forest analysis highlighted that ozone parameters were the most important predictors influencing the tree growth. Significantly lower contents of chlorophyll were found in oak species in significantly defoliated trees (defoliation > 25%) and for pine species was vice versa. Accumulated H2O2 was reflected in the presence of lipid peroxidation in all species. Significant differences were found for significantly defoliated holm oak and Aleppo pine trees, while for pubescent oak it was found for low defoliated trees. Activation of all examined antioxidative enzymes in all species was determined. Ascorbate peroxidase enzyme activity could be considered as an indicator of stress in trees for examined species. The plants were found to be under stress although no visible damage was observed.