A total of 45 bacteria were isolated from root nodules of sulla (Hedysarum coronarium L.) in Tunisia and tested for their tolerance to NaCl, alkaline pH and PEG-induced water stress. Tolerance limits varied from 150 to 700 mM for NaCl, from 9 to 10.5 for alkaline pH and from −0.5 to −0.95 MPa for PEG-induced stress. Three effective isolates with variable tolerance were retained to study the effect of water deficiency. The 16S rRNA gene sequencing showed that the closest relative to the three isolates was Rhizobium sullae strain IS 123T. Plants inoculated with the moderately tolerant strain Hc14 showed the highest shoot dry yield at 75% FC; however, for lower soil moisture levels, strain Hc14 was quite similar to the most tolerant strain Hc5. By contrast, plants inoculated with the most sensitive strain Hc1 showed the lowest nodule number and shoot dry yield. At high water deficiency (20% FC), strains Hc5 and Hc14 were still able to induce nodules; however, strain Hc1 failed. Strains Hc5 and Hc14 were then assayed in a non-irrigated field trial. The results confirmed the usefulness of these strains as inoculants under water deficiency. However, other trials should be conducted in other sites to further confirm these results.