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Drought stress is one of the most important factors limiting plant growth; in particular, water is regarded as a major problem in symbiotic nitrogen fixation for legume growth. The adverse effects of water stress on the rhizobial symbiosis of common bean genotypes CocoT and Flamingo were investigated in field conditions. Common bean plants were inoculated with rhizobia strains: Rhizobium tropici CIAT899 or Rhizobium etli 12a3, and grown under field conditions, plants were spray irrigated until the first flower was observed on set. Irrigation was stopped for 20 days in plants submitted to water stress. The enzyme-linked immunosorbent assay (ELISA) technique was used with polyclonal antibody to assess the occupancy in nodule of the rhizobia used for inoculation. Under water stress, a significant decrease in nodule population, nodules biomass, shoot content of nitrogen, growth and chlorophyll with all symbioses, whereas proline accumulation increased. The interaction between symbioses and water stress for all parameters was significant. Overall, 12a3 was more efficient than CIAT899 for Flamingo, though not for CocoT. It is concluded that symbiosis between Flamingo and 12a3 has potential for application in field under water stress in desert soil.