Ecosystems remove ozone from the troposphere through both stomatal and non-stomatal depositions. The portion of ozone taken up through stomata has an oxidative effect causing damage. We used a multi-year dataset to assess ozone deposition to a ponderosa pine plantation near Blodgett Forest, Georgetown, California. Environmental parameters, water and ozone concentrations and fluxes were measured continuously from January 2001 to December 2006. High levels of ozone concentrations (up to 100 ppb) were observed during the spring–summer period, with corresponding high levels of ozone fluxes (up to 30 μmol m−2 h−1). During the summer season, we calculated that a large portion of the total ozone flux was due to non-stomatal processes, which is in agreement with previous studies suggesting that chemical reactions with BVOCs (biogenic volatile organic compounds) emitted by the ecosystem are mainly responsible for this ozone flux. We also report here the first direct measurement of BVOC + ozone oxidation products, confirming that ozone loss process is occurring below our flux measurement height. We analyzed the correlations of common ozone exposure metrics based on accumulation of concentrations (AOT40 and SUM0) with ozone fluxes (total, stomatal and non-stomatal). Stomatal flux, which is considered responsible for ozone damage, showed a weaker correlation with ozone concentrations than non-stomatal flux during summer and fall seasons. The non-stomatal flux is more strongly correlated with ozone concentration because BVOC emission and ozone concentration both increase with temperature. We suggest that AOT40 and SUM0 are poor predictors of stomatal ozone uptake, and that a physiologically based metric would be more effective.