Climate change results in increased attention to factors determining the dynamics of biogeochemical processes in the active layer of biosphere (seasonally thawing/freezing soils) at the boundary with permafrost. There are geological, geomorphic, and weather conditions associated with atmospheric precipitation, which determine the differences in the segregation and the thawing depth of permafrost in various regions. The research area is the Bureya River Basin with discontinuous permafrost within unique landscape units: Mari. They are formed in swampy and poorly drained areas where the active soil layer is in contact with permafrost, and they exert a direct impact on the quality of surface waters. The results of the study include data on the chemical composition of water in tributaries of different orders; spectral characteristics of soluble organic matter (OM) in water extracts (WEs) of soils from different horizons of the active layer; and the assessment of the activity of microbial complexes in relation to humic substances (HSs), depending on the permafrost depth. The heterogeneity of landscapes is an important factor, influencing the transport of OM into watercourses. Microbial complexes of the active layer involved in the transformation of HSs play a decisive role in changing the composition of soluble OM. It is experimentally shown that temperature affects the qualitative composition of metabolism products of HSs, including the ratio of aliphatic and aromatic fragments to chromophoric groups responsible for the color of natural waters.