The aim of the present study was to analyze the growth and physiological performance of two coexisting species, Trifolium fragiferum, and Trifolium repens, under the effect of NaCl and rhizobial symbiosis. Seeds of T. fragiferum and T. repens were collected from populations in the wild, and plants were cultivated in an automated greenhouse, two plants per container. Three basic types of planting were performed: (1) both plants were T. fragiferum (single species), (2) one T. fragiferum and one T. repens (species coexistence), (3) both plants were T. repens (single species). For every basic type, three subtypes were made: (1) non-inoculated, (2) inoculated with rhizobia taken from T. fargiferum, (3) inoculated with rhizobia taken from T. repens. For every subtype, half of the containers were used as control, and half were treated with NaCl. Shoot fresh mass of plants was significantly (p < 0.001) affected by species coexistence, inoculant, and NaCl. Three significant two-way interactions on plant shoot growth were found: between species coexistence and NaCl (p < 0.001), inoculant and species (p < 0.05), and NaCl and species (p < 0.001). A significant three-way interaction between inoculant, NaCl, and species (p < 0.001) indicated different responses of shoot growth of the two species to inoculant type and NaCl. NaCl treatment was an important factor for T. fragiferum, resulting in better growth in conditions of species coexistence, but the positive effect of bacterial inoculant was significantly more pronounced. A decrease in peroxidase activity in leaves was a good indicator of relative NaCl tolerance, while the absence/presence of rhizobial inoculation was reflected by changes in leaf chlorophyll concentration and photochemical activity of photosystem II. It can be concluded that interaction between biotic and abiotic factors affected the outcome of the coexistence of the two Trifolium species. Distribution of T. fragiferum in sea-affected habitats seems to be related to a higher competitive ability with allied species at increased substrate salinity, based on better physiological salinity tolerance.