Large branchiopods are threatened worldwide by the loss and degradation of their temporary aquatic habitats owing to drainage and intensive agriculture. Sound ecological knowledge of their diversity and distribution is a prerequisite to formulate effective conservation measures. In the present study, large branchiopods were collected from 82 temporary freshwater pools belonging to five habitat types in Kiskunság (Hungary). Dormant propagule bank analysis complemented the field survey. Eleven species were found, with large branchiopods occurring in more than half of the study systems. The high regional species richness and occurrence frequency of large branchiopods make Kiskunság a true ‘hot spot’ of large branchiopod diversity. The local environment was more important than spatial factors (isolation) in explaining the presence of the most common species. Dispersal was most likely not limiting for the large branchiopods in the study area and colonisation success of different species was differentially affected by local conditions, possibly invertebrate predation risk and hydroperiod. Meadow pools and wheel tracks contributed most to regional species richness through the presence of rare and exclusive species. To conserve branchiopod diversity, we stress the importance of high habitat diversity in the landscape and the need to conserve neglected habitats such as wheel tracks.