Soil microorganisms, such as plant growth-promoting rhizobacteria (PGPR), play crucial roles in plant growth, but their influence on plant water relations remains poorly explored. We studied the effects of native soil microorganisms and inoculation with the PGPR strain Aur6 of Pseudomonas fluorescens on water stress responses of seedlings of the drought-avoiding Pinus halepensis Mill. and the drought-tolerant Quercus coccifera L. Plant growth, nutrient concentrations and physiology (maximum photochemical efficiency of photosystem II (PSII; F_v/F_m), electron transport rate (ETR), stomatal conductance (g_s) and predawn shoot water potential (Ψ_PD)) were measured in well-watered plants, and in plants under moderate or severe water stress. Inoculation with PGPR and native soil microorganisms improved tree growth, and their interactions had either additive or synergistic effects. Both F_v/F_m and ETR were significantly affected by PGPR and native soil microorganisms. Marked differences in g_s and Ψ_PD were found between species, confirming that they differ in mechanisms of response to water stress. A complex tree species × treatment interactive response to drought was observed. In P. halepensis, F_v/F_m and ETR were enhanced by PGPR and native soil microorganisms under well-watered conditions, but the effects of PGPR on Ψ_PD and g_s were negative during a period of water stress. In Q. coccifera, F_v/F_m and ETR were unaffected or even reduced by inoculation under well-watered conditions, whereas Ψ_PD and g_s were increased by PGPR during a period of water stress. Our results indicate that microbial associates of roots can significantly influence the response of tree seedlings to drought, but the magnitude and sign of this effect seems to depend on the water-use strategy of the species.