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Small soda lakes represent one of the most vulnerable ecosystem types due to their high hydrological sensitivity to climate change and anthropogenic interventions. Since diatoms are excellent bioindicators, determining the -diversity and the structuring dynamics of diatom metacommunities can provide valuable information for conservation planning for soda pans. In this study, two diatom metacommunities were surveyed monthly during a one-year period from distinct regions of the Carpathian basin: the Fert-Hansag National Park (FH) between 2013 and 2014, and the Danube-Tisza Interfluve (DT) between 2014 and 2015. We explored whether -diversity of diatom assemblages in the two regions is enhanced by species turnover or nestedness (related to richness differences) and investigated the role of deterministic and stochastic processes in shaping -diversity patterns. Furthermore, we evaluated the contribution of environmental variables, geographic distance and temporal variation to community structure. High -diversity (>90%) was revealed for both metacommunities, and was maintained primarily by species turnover. Within the metacommunity of the DT where the natural hydrological cycle of soda pans is not disturbed, diatom communities assembled mainly due to the selection force of environment at a spatiotemporal scale. In the soda pans located in the habitat reconstruction area of the FH, besides species-sorting, significant temporal variation in community structure appeared as a result of water management and periodic water supply. Our results point to the need for a conservation management strategy which maintains the natural hydrological regime of small saline lakes, and therefore their habitat heterogeneity which is of high conservation value.