The compartmentation of ions in salinity‐stressed 6‐week‐old alfalfa seedlings was investigated in two cultivars, Batini (moderately salinity tolerant) and Hunter River (salinity sensitive). Both cultivars were grown under field conditions during the cool season (20–25°C) and the warm season (35–46°C). Two saline solutions (6.4 and 12.2 dS m‐1) were prepared by dissolving the required quantity of NaCl in half‐strength Hoagland solution. Tap water (0.8 dS m‐1) served as control. Plants were irrigated twice a week with saline solutions, commencing 3 weeks after seedling emergence. The seedlings were separated into leaf (including petiole), stem, and root after 6 weeks of growth and analysed for phosphorus (P), potassium (K), calcium (Ca), magnesium (Mg), sodium (Na), chloride (Cl), and micronutrients [copper (Cu), boron (B), zinc (Zn), manganese (Mn), and iron (Fe)]. The concentration of P and K in the plant tissue increased with increase in temperature, while Ca and Mg concentrations were depressed. Increase in salinity, in general, resulted in decreased accumulation of all ions, including micronutrients. Hunter River maintained the same pattern of ion compartmentation (root<stem<leaf) for Na and Cl, whereas in Batini a different pattern was obtained for Na (stem<leaf<root). Since the compartmentation pattern of ions in Batini is different for Na and not Cl, it appears that compartmentation of Na may be an important factor in salt tolerance.