The question of the effect of the anion type on halophyte salt tolerance and ion accumulation is still far from the necessary generalization due to the lack of comparative studies. The aim of the present study was to compare the relatively long-term effect of treatment with various salts formed by different anions on the growth and ion accumulation of several halophyte species in controlled conditions. The main experiments with the largest variety of individual salt types were performed with Cochlearia officinalis L. and two cultivars of Limonium sinuatum (L.) Mill. In addition, experiments with Lobularia maritima (L.) Desv., Plantago maritima L., and Tripolium pannonicum (Jacq.) Dobrocz. focused on the comparison of neutral (NaCl) and alkaline (NaHCO3) salts as well as NaNO3. Acetate salts appeared to be the most toxic, with only Plantago and Tripolium plants being able to withstand full treatment while having a pronounced inhibition in growth. Only the two Limonium cultivars were more susceptible to treatment with alkaline salts in comparison to that with neutral salts. In treatments with alkaline salts, the ion accumulation potential was lower in comparison to plants treated with chlorides and nitrates. It can be concluded that the type of anion is a significant determinant of salinity tolerance and ion accumulation in halophytes, but a high genotype dependence of the responses makes it difficult to generalize the obtained results.