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The eastern part of the Pamir Mountains, located in Central Asia, is characterized by great climatic continentality and aridity. Wetlands developed in this hostile region are restricted to spring areas, terraces of shallow lakes or floodplains along rivers, and provide diversified ecosystem services e.g. as water reservoirs, refugia for rare species and pastures for domestic cattle. These ecosystems are particularly susceptible to climate changes, that in the Pamir Mountains result in increased temperatures, intense permafrost/glacial melt and alterations of precipitation patterns. Climatic changes affect pasture management in the mountains, causing overutilization of sites located at lower elevations. Thus, both climate and man-induced disturbances may violate the existing ecological equilibrium in high mountain wetlands of the Eastern Pamir, posing a serious risk to their biodiversity and to food security of the local population. In this context, we sought to assess how environmental drivers (with special focus on soil features and potential water sources) shape the distribution and diversity of halophytic plant communities developed in valleys in the Eastern Pamir. This task was completed by means of a vegetation survey and comprehensive analyses of habitat conditions. The lake terraces and floodplains studied were covered by a repetitive mosaic of plant communities determined by differences in soil moisture and salinity. On lower, wetter sites, this patchwork was formed by Blysmus rufus dominated salt marshes, saline small sedge meadows and saline meadows with Kobresia royleana and Primula pamirica; and on drier, elevated sites, by endemic grasslands with Hordeum brevisubulatum and Puccinellia species and patches of xerohalophytic vegetation. Continuous instability of water sources and summer droughts occurring in the Pamir Mountains may lead to significant structural and functional transformations of described wetland ecosystems. Species more tolerant to decreased soil moisture and/or increased soil salinity will expand, leading to alterations of ecosystem services provided by the Pamirs’ wetlands. The described research will help to assess the current state of the wetlands and to predict directions of their future changes.