In two arid/semiarid regions, we studied diversity of algae in lakes and pools with salinity ranging from 0.1‰ up to 39‰ In plankton and periphyton of 34 lakes in northern Kazakhstan, we found 252 species belonging to 113 genera of 8 algal divisions. In 24 pools with experimental salinity ranges in the Negev desert of Israel, we recorded 86 species from 47 genera of 6 algal divisions. The dominant groups of both arid regions are represented by widespread species of diatoms, green algae, and cyanobacteria in similar proportions. Alkaliphiles among the indicators of acidification and betamesosaprobionts among the indicators of saprobity prominently prevail in both regions. The indices of saprobity in lakes (1.48–2.7) and in pools (0.75–2.18) reflect a low-trophic loading. Oligohalobes-indifferents are most common in both arid regions. Cluster analysis based on data containing 420 species revealed 9 clusters, of which the highly diverse communities of low mineralized lakes and pools and the low diversity communities of highly-mineralized lakes and pools are separated at the highest dissimilarity level. CCA analysis revealed correlation of the algal species diversity preferences with salinity level in lakes in Kazakhstan and in pools of Israel, which are more impacted by arid factors. These results point to mineralization being the most important variable defining the diversity levels irrespective of the type and location of reservoirs in the arid regions.