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In the context of global climate change, a significant increase in the active layer thickness (ALT) of permafrost is expected in the current century. This process has been observed by researchers over the past few decades. If the current climate trend continues, an increase in ALT may have a significant impact on the concentration of organic matter in Arctic river waters. The relationship between the thickness of the seasonally thawed layer of permafrost and the concentration of dissolved organic matter in river waters has been explored using clustering, one-way ANOVA, and cross-tabulation analysis. The data set for analysis included original details on the content of organic matter in the rivers of Eastern Siberia (in terms of COD, BOD5, and the color of the water), phytoplankton abundance and biomass, and data on the permafrost active layer thickness (ALT) in the catchments. It was revealed that in the areas of catchments where the ALT is deeper, the content of organic matter in the rivers is lower than in areas with a shallow, seasonally thawed permafrost. Our results are consistent with the existing conceptual model of the influence of ALT on the chemistry of river waters in the cryolithozone. This knowledge is important for predicting the chemical composition of the Arctic rivers, eutrophication, and the rate of inflow of dissolved solids into the Arctic Ocean under the current conditions of ALT deepening.