Soil moisture and water stress play a pivotal role in regulating stomatal behaviour of plants; however, in the last decade, the role of water availability was often neglected in atmospheric chemistry modelling studies as well as in integrated risk assessments, despite through stomata plants remove a large amount of atmospheric compounds from the lower troposphere. <br><br> The main aim of this study is to evaluate the effect of soil water limitation on stomatal conductance and assess the resulting changes in atmospheric chemistry testing various hypotheses of water uptake by plants in the rooting zone; following the main assumption that roots maximize water uptake, i.e. they adsorb water at different soil depths depending on the water availability, we improve the dry deposition scheme within the chemistry transport model CHIMERE. <br><br> Results highlight how dry deposition significantly declines when soil moisture is used to regulate the stomatal opening, mainly in the semi-arid environments: in particular, over Europe the amount of ozone removed by dry deposition in one year without considering any soil water limitation to stomatal conductance is about 8.5 Tg O<sub>3</sub>, while using a dynamic layer that ensures plants to maximize the water uptake from soil, we found a reduction of about 10 % in the amount of ozone removed by dry deposition (~ 7.7 Tg O<sub>3</sub>). Despite dry deposition occurs from top of canopy to ground level, it affects the concentration of gases remaining into the lower atmosphere with a significant impact on ozone concentration (up to 4 ppb) extending from the surface to the upper troposphere (up to 650 hPa). <br><br> Our results shed light on the importance of improving the parameterizations of processes occurring at plant level (i.e. from the soil to the canopy) as they have significant implications on concentration of gases in the lower troposphere.