This research assesses the possibility of using unique special observations data at the Suntar-Hayata station in Eastern Siberia (it was operating from 1957-1959 under the program of the International Geophysical Year) to develop and apply methods for modelling hydrological processes in the permafrost zone under conditions of poor information content to identify flow changes and understand the causes of their occurrence. In the course of the work, the results of special observations were analysed, the parameters of the hydrological model, Hydrograph, characterizing the landscapes of the Eastern Siberia, were developed. The parameters were verified in the modelling of state variables at the Suntar River basin (7680 km2) and the modelled streamflow compared with the observed values (1957-1964). The results of the simulation were found to be satisfactory. At the next stage, the water balance and hydrographs were simulated for watersheds over the period 1966-2012. The results of the simulation are satisfactory too. It allows us to conclude that the Hydrograph model can reproduce the processes occurring in the catchment area allowing it to be used in the flow modelling of the study area. To study the possibility of modeling the observed flow changes, the flow simulation for the period 1966-2012 was carried out. Significant increasing trends in simulated runoff were seen in May-11.3 mm or 118%, in September-10.2 mm or 38.1%, in October-1.3 mm or 33.3% and in November-0.35 mm or 35.9%. These trends are comparable to trends seen in the observed flow values. The simulation confirmed the theory that runoff changes are due to an increase in the proportion of liquid precipitation during the transition months. The liquid precipitation increased by an average of 13.6 mm for the Suntar River basin, which is similar to to the observed streamflow value trend in September of about 10 mm. Thus, the use of modelling methods can be a reliable tool for predicting runoff changes in permafrost. The method can be used to study the causes of runoff and variable state changes in other basins in the permafrost environment.