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The flooding on the Lena River near city Yakutsk is driven by two main factors – snowmelt runoff and ice jam formations, maximum water levels are exceeded 10 m above the low-water level. There is the statistically significant increase in maximum water discharges in the section of the river Lena under consideration (gauge Tabaga, basin area 897000 km2); at the same time, the ice jam occurrence and duration of maximum water flow are became lower. The simulation of the flooding for the long-term period 1982-2016 has been conducted using the two-dimensional hydrodynamic model STREAM_2D, taking into account daily water discharges, ice jams formation, river channel changes. Results of modelling has shown good correspondence of modeled and observed daily water levels (Nash - Sutcliffe criteria for all sub-periods was above 0.90) and inundations zones (more than 20 satellite images were analyzed). The pioneering task by comparing the maps of the flood duration obtained from the results of modeling with data of landscape indication was solved and the correspondence of the main zones of the flooding duration based on two independent methods were received. The significant changes in the flooding characteristics was identified and amounted to about 8% in terms of increasing the inundation area and the average depth of flooding. The meaningful changes in the duration and the frequency of flooding was detected, and they are reflected in the distribution of plants communities according to landscape indication methods. The research was supported by the RFBR №17-05-1230 (flooding modeling) and №18-05-60021 (hydrological data analysis).