Alfalfa (Medicago sativa L.) is one of the most important forage crops and has high protein and highly digestible fibre contents. It can be cultivated in moderate salt-alkaline soils and has been widely cultivated as an economic crop worldwide. We quantified the effects of salt (1:1 molar ratio of NaCl to Na2SO4, pH 7.01–7.05) and alkali (1:1 molar ratio of NaHCO3 to Na2CO3, pH 9.80–10.11) stresses on germination, growth, photosynthesis and ion accumulation in alfalfa. The results showed that both stresses significantly reduced germination and radicle elongation, indicating that alfalfa was relatively sensitive to both stresses during seed germination and early seedling growth stages. The relative growth rate, water content, chlorophyll content, intercellular CO2 concentration, stomatal conductance, net photosynthetic rate (PN) and transpiration rate decreased slightly with increasing salinity under salt stress, but were markedly reduced under alkali stress. Conversely, water use efficiency increased with increasing salinity under both stresses. The Na+ content increased and the K+ content decreased with increasing salinity under both stresses, indicating competitive inhibition between the absorption of Na+ and K+. Intracellular imbalance of Na+ and K+ caused by high pH of alkali stress might be one of the reasons for the visible decrease in PN. Both Ca2+ and Mg2+ contents decreased with increasing salinity under both stresses. Our study found that the deleterious effects of alkali stress were more severe than those of salt stress.