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Considering the ongoing loss of aquatic habitats, anthropogenic ponds are gaining importance as substitute habitats. It is therefore important to assess their functioning in comparison to their natural precursors. Here we assess the biodiversity value of sodic bomb crater ponds by comparing their gamma diversity to that of natural reference habitats, astatic soda pans, and assess their importance on the landscape level by studying alpha and beta diversity. We studied aquatic organisms ranging from algae to vertebrates in a dense cluster of 54 sodic bomb crater ponds in Central Europe. Despite the overall small area of the pond cluster, gamma diversity was comparable to that found in surveys of natural habitats that encompassed much wider spatial and temporal scales. We also found a considerable number of species shared with reference habitats, indicating that these anthropogenic habitats function as important refuge sites for several species that are associated with the endangered soda pans. Moreover, we found a number of regionally or worldwide rare species. Among the components of beta diversity, species replacement dominated community assembly. Individual ponds contributed similarly to beta diversity in terms of replacement, being equally important for maintaining high gamma diversity and emphasising the role of the pond network rather than individual ponds. This pattern was seen in all studied groups. Bomb crater ponds therefore acted as important contributors to aquatic biodiversity. Considering the tremendous losses of ponds throughout Europe, anthropogenic ponds should be taken into consideration in nature conservation, especially when occurring in pond networks.