Global warming is heating the Antarctic circumpolar deep water (CDW), which comes into direct contact with the diverse and abundant macrobenthic communities thriving on the continental shelf of the Weddell Sea (WS). A set of 16 current meters deployed along more than 3000 km coastline revealed that tidal currents drive CDW intrusions onto the WS continental shelf and they can increase the temperature near the seabed by ~2.7 °C. The ongoing ocean warming trend may expose macrobenthic assemblages to ambient temperatures>2 °C by the end of the century with dramatic consequences for communities which have evolved during millions of years in near geophysical isolation under rather constant environmental conditions with temperatures<0 °C. These stenothermal communities have long generation times (therefore, reduced opportunity to mutate) and require hundreds of years for adaptation. Results from 135 benthic stations along the study area showed that macrobenthic communities in the southeastern section of the WS are the most vulnerable to the increase of temperature near the seabed given their high component of sessile organisms. Besides a dramatic marine biodiversity loss, the eventual demise of these communities, which provide habitat structure for a large number of species that can build up>87 g C m−2, will cause the liberation of thousands of tons of carbon to the environment. Macrobenthic communities colonizing the recently opened shelf in the Larsen A and B bays may not have the chance to reach the type of mature assemblage inhabiting the eastern WS shelf. The highest temperatures derived from CDW intrusions were recorded in the Filchner-Ronne region, suggesting that the consequences of the thermal impact could develop faster here than in the rest of the WS. Thus, these macrobenthic communities may show the effects of warming earlier than those thriving in other regions of the WS shelf. Global warming seriously threats the abundant and highly diverse macrobenthic communities of the Antarctic continental shelf.