Despite the high conservation value of intermittent soda pans, these habitats were mostly targeted by small‐scale studies and little is known about their microscopic fauna. We sampled all the remaining 110 representatives of this habitat type (including recently restored ones) in Europe in an area covering approximately 125 000 km2. We analyzed spring and summer zooplankton species composition including rotifers, copepods, and cladocerans. We found 105 Rotifera, 26 Cladocera, and 26 Copepoda taxa, with local species richness ranging between 1 and 38 taxa. Alpha diversity was comparable in the two main groups (Rotifera, Crustacea), while beta and gamma diversity was higher in rotifers. The most frequently occurring zooplankters were crustaceans, while rotifer taxa were rarer as the most frequent species inhabited less than half of the pans. Dominance of the natronophilic Arctodiaptomus spinosus proved to be a reliable indicator for high quality soda pans. We concluded that the most typical soda pan zooplankton communities developed by early summer, in the concentrated pans, thus we would suggest considering this period as a reference for ecological state monitoring, and especially for evaluating the success of soda pan rehabilitations or reconstructions with the help of zooplankton. Based on these criteria, restorations could be considered only moderately successful.