The West Antarctic Peninsula is one of the fastest warming regions on Earth. Faster glacier retreat and related calving events lead to more frequent iceberg scouring, fresh water input and higher sediment loads, which in turn affect shallow water benthic marine assemblages in coastal regions. In addition, ice retreat creates new benthic substrates for colonization. We investigated three size classes of benthic biota (microbenthos, meiofauna and macrofauna) at three sites in Potter Cove (King George Island, West Antarctic Peninsula) situated at similar water depths but experiencing different disturbance regimes related to glacier retreat. Our results revealed the presence of a patchy distribution of highly divergent benthic assemblages within a relatively small area (about 1 km2). In areas with frequent ice scouring and higher sediment accumulation rates, an assemblage mainly dominated by macrobenthic scavengers (such as the polychaete Barrukia cristata), vagile organisms and younger individuals of sessile species (such as the bivalve Yoldia eightsi) was found. Macrofauna were low in abundance and very patchily distributed in recently ice-free areas close to the glacier, whereas the pioneer nematode genus Microlaimus reached a higher relative abundance in these newly exposed sites. The most diverse and abundant macrofaunal assemblage was found in areas most remote from recent glacier influence. By contrast, the meiofauna showed relatively low densities in these areas. The three benthic size classes appeared to respond in different ways to disturbances likely related to ice retreat, suggesting that the capacity to adapt and colonize habitats is dependent on both body size and specific life traits. We predict that, under continued deglaciation, more diverse, but less patchy, benthic assemblages will become established in areas out of reach of glacier-related disturbance.