This study investigated a wide range of morphological and physiological responses of burr medic (Medicago polymorpha L. cv. Scimitar) and balansa clover (Trifolium michelianum L. cv. Frontier) to different levels of salinity. Balansa clover and burr medic plants were grown in the greenhouse at 25°C day temperature and 16°C night temperature. Salt treatments were applied 6 weeks after germination, and plants were grown for a further 6 weeks before harvest. The salt treatments included a control, 20 mm, 40 mm, and 80 mm of NaCl. The shoot biomass yield was significantly affected by the species × salt interaction (P = 0.04). For balansa clover, the shoot biomass yield was greatest for the control treatment and lowest for the 20 mm NaCl treatment. For burr medic, the shoot biomass yield did not differ among salt treatments. Sodium (Na+) and potassium (K+) concentrations in leaves and stems increased with salinity. Compared with a non-saline control, sodium concentration in leaves in the 80 mm NaCl treatment was 3-fold higher for balansa clover and 2-fold higher for burr medic. Under various saline treatments, leaf Na+/K+ ratio stayed relatively constant in balansa clover (0.3–0.4) and burr medic (0.4–0.5), whereas stem Na+/K+ ratios for both species increased with salinity. The most sensitive parameters to salinity were Na+/K+ and Na+/Ca2+ ratios, whereas biomass, chlorophyll fluorescence, net photosynthesis, stomatal conductance, transpiration, and δ13C and δ15N discrimination were least sensitive. Therefore, accumulation of sodium in the plant tissues did not reach the threshold for causing reduction in growth.