The paper considers the qualitative characteristics (chemical composition of waters and sediments, biological diversity) of the Lena runoff and their transformation as a result of the biogeochemical processes taking place in the delta region. The hydrological, hydrochemical, geochemical (chemical composition of river sediments), and hydrobiological description of the delta branches at the current stage has been provided. The Lena delta branches are characterized by a wide variety of water discharge values and hydrodynamic conditions. It has been revealed that the hydrochemical composition of the delta is specific due to the dominance of hydrocarbonates and calcium ions, pH 6.9-7.9, high oxygen saturation conditions (more than 100 % sat.) throughout the water column because of wind activity, high concentrations of dissolved silica (1.1-2.7 mg/L) and iron (0.01-0.07 mg/L) if compared to the world's mean values in natural freshwater bodies, and low concentrations of trace elements (mainly below the detection limits). The concentrations of nitrates and phosphates have been estimated in the range of 2.6-34.7 µg/L and 3.1-26.2 µg/L, respectively. The bottom and suspended sediments have been assigned to the siliceous type (Si/Al varies from 4.2 to 18 µg/L). The results of the analysis of hydrodynamic conditions, hydrobiological features, geochemical indices, as well as data of the statistical factor analysis, have shown chemical elements redistribution dependencies. Several factors determining the chemical composition of water and sediments in the Lena River delta have been distinguished. The interpretation of these factors reflects the influence of river catchment area, cryogenic processes in the river delta, and biogeochemical processes. Based on the modern multidisciplinary research performed in the Lena delta, it has been demonstrated that processes leading to an inhomogeneous distribution of chemical elements between water (dissolved fraction), suspended matter, and bottom sediments occur in the delta of the river.