The results of the study of the influence of the deep factor on the process of melting of the ice cover of the Arctic Ocean and the formation of dangerous natural phenomena are presented. The peculiarities of the structure of the earth’s crust contributing to the ice destruction are visualized based on the interpretation of anomalies of the magnetic field and gravity. Density and magnetic sections of the bottom structures are constructed taking into account seismic and seismological data. Two-dimensional density calculations of the Arctic crust density have been performed to detect fluid-saturated layers. Analysis of satellite observations of ice condition together with interpretation of gravity and magnetic data made it possible to identify natural phenomena of endogenous origin, caused by influence of thermo fluid flows of the earth’s crust. The study of annual and seasonal changes in the thickness of multiyear ice over the period 2007–2020 has shown that a decisive role in the thawing process is played by fluid-supplying channels of deep-seated fault zones. The role of an endogenous factor in the destruction of ice of different ages and in the emergence of dangerous phenomena in the areas of hydrate development has been revealed. This makes it possible to predict the localization of zones of variability in the thickness of multiyear ice, the nature of the destruction of its edges and reduce the risks of navigation.