Summer hydrographic data (1920–2009) show a dramatic warming of the bottom water layer over the eastern Siberian shelf coastal zone (<10 m depth), since the mid-1980s, by 2.1°C. We attribute this warming to changes in the Arctic atmosphere. The enhanced summer cyclonicity results in warmer air temperatures and a reduction in ice extent, mainly through thermodynamic melting. This leads to a lengthening of the summer open-water season and to more solar heating of the water column. The permafrost modeling indicates, however, that a significant change in the permafrost depth lags behind the imposed changes in surface temperature, and after 25 years of summer seafloor warming (as observed from 1985 to 2009), the upper boundary of permafrost deepens only by ∼1 m. Thus, the observed increase in temperature does not lead to a destabilization of methane-bearing subsea permafrost or to an increase in methane emission. The CH4 supersaturation, recently reported from the eastern Siberian shelf, is believed to be the result of the degradation of subsea permafrost that is due to the long-lasting warming initiated by permafrost submergence about 8000 years ago rather than from those triggered by recent Arctic climate changes. A significant degradation of subsea permafrost is expected to be detectable at the beginning of the next millennium. Until that time, the simulated permafrost table shows a deepening down to ∼70 m below the seafloor that is considered to be important for the stability of the subsea permafrost and the permafrost-related gas hydrate stability zone.