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Beaded channels, consisting of deepened and widened pools and connecting narrow runs, are common type of low order channels in permafrost regions. Recent studies have shown that beaded channels are very important for connecting alluvial rivers with headwater lakes allowing fish passage and foraging habitats, as well as regulating river runoff. Beaded channels are known as typical thermokarst landforms; however, there is no evidence of their origin and formative processes. Geomorphological analyses of beaded channels have been completed in several permafrost regions including field observations of Shestakovka River in Central Yakutia. The study aims to recognize the modern exogenic processes and formative mechanisms of beaded river channels. We show that beaded channel of Shestakovka River form in the perennially frozen sand with low ice content, leading us to hypothesize that thermokarst is not the main process of formation. Due to the significant volume of water, the pools don’t freeze over entirely during winters, even under harsh climatic conditions. As a result, lenses of pressurized water remain under surface ice underlain by perennially thawed sediments. The presence of thawed sediments under the pools and frozen sediments under the runs leads to uneven thermoerosion of the riverbed during floods, providing the beaded form of the channel. In addition, freezing of pools during winter leads to pressure increasing under ice cover and formation of ice mounds, which crack several times during winter leading to disturbance of riverbanks. Many 1st to 3rd order streams have a specific transitional meandering-to-beaded form resembling the shape of unconfined meandering rivers, but consisting of pools and runs. However, such channels exhibit no evidences of present-day erosion of concave banks and sediment accumulation at the convex banks as typically being observed in normally meandering rivers. Such forms of channels indicates that their formation occurred by the greater channel-forming flow discharges in the past. Transition to the beaded channel planform took place only later, presumably as a result of climate changes. Reduction of water runoff and freezing over of taliks leaded to activation of cryogenic processes (thermokarst, uneven thermoerosion, disturbance of riverbanks during the cracking of ice mounds).