Stomata control gas exchanges between the plant and the atmosphere. How natural variation in stomata size and density contributes to resolve trade‐offs between carbon uptake and water‐loss in response to local climatic variation is not yet understood. We developed an automated confocal microscopy approach to characterize natural genetic variation in stomatal patterning in 330 fully‐sequenced Arabidopsis thaliana accessions collected throughout the European range of the species. We compared this to variation in water‐use efficiency, measured as carbon isotope discrimination (δ13C). We detect substantial genetic variation for stomata size and density segregating within Arabidopsis thaliana. A positive correlation between stomata size and δ13C further suggests that this variation has consequences on water‐use efficiency. Genome‐wide association analyses indicate a complex genetic architecture underlying not only variation in stomata patterning but also to its co‐variation with carbon uptake parameters. Yet, we report two novel QTL affecting δ13C independently of stomata patterning. This suggests that, in A. thaliana, both morphological and physiological variants contribute to genetic variance in water‐use efficiency. Patterns of regional differentiation and co‐variation with climatic parameters indicate that natural selection has contributed to shape some of this variation, especially in Southern Sweden, where water availability is more limited in spring relative to summer. These conditions are expected to favor the evolution of drought avoidance mechanisms over drought escape strategies.