The accumulated stomatal ozone (O3) uptake over a threshold (Phytotoxic Ozone Dose POD6), calculated by an ozone deposition model, has been shown to be the most appropriate metric to quantify negative effects of O3 on food crops. In this study we used data of 13 sites in different regions of Switzerland with multiple years of O3 measurements to quantify the stomatal O3 uptake and the related yield loss of wheat and potato. Flux patterns for different years were calculated with the DO3SE model to disentangle the influence of contrasting seasonal environmental conditions. Regional and inter-annual differences in meteorological conditions led to considerable variations in soil water conditions and the POD6 values for wheat. Potato stomatal uptake was much less influenced by soil water and showed a more even distribution of POD6 values across sites and years. The estimated nationally and temporally average yield loss was 3.2 ± 1.2% for wheat and 2.4 ± 0.8% for potato, calculated based on an area weighting.It was found that soil water deficit, observed frequently in the western part of Switzerland, had a large attenuation effect on stomatal O3 uptake by wheat and on corresponding yield losses. This highlights the importance of including soil moisture limitation in O3 uptake modelling even in moist climatic regions. The comparison of modelled evapotranspiration with water flux measurements over a wheat field showed a reasonable agreement concerning the temporal pattern and the magnitude. But it is also concluded that the DO3SE soil moisture module will need further testing and adaptation to improve accuracy of the model in dryer conditions.