The western Antarctic Peninsula is one of the fastest warming regions on Earth, leading inter alia to glacier retreat, increasing glacial discharge and ice-scouring. While glacier retreat lays bare new settling ground, glacial discharge and ice-scouring are known factors modifying the structure of coastal benthic communities. However, effects on benthic biogeochemical processes like benthic carbon cycling remain largely unknown. To assess this question, diver-operated in situ measurements and sampling were performed at Potter Cove (King George Island, Antarctic Peninsula) at three sites, which differ in intensity of glacial discharge, frequency of ice-scouring and time since the Fourcade glacier retreated. Total and diffusive oxygen uptake (TOU and DOU), inorganic nitrogen fluxes and phosphate fluxes were determined and sediment characteristics and abundances of the dominant bivalve Laternula elliptica analysed. At the glacier front (recently glacier-free, high glacial discharge, high ice-scouring frequency) TOU, inorganic nitrogen and phosphate fluxes were lowest, while the highest fluxes were determined at the oldest glacier-free site (intermediate glacial discharge, intermediate ice-scouring frequency). In contrast, DOU revealed the opposite trend. At all sites TOU exceeded DOU at least five-fold, indicating that biogeochemical fluxes in Potter Cove were primarily mediated by macrofauna. This was partly supported by the trend of abundances of Laternula elliptica. Furthermore, sediment characteristics changed from silt-dominated at the glacier front to sand-dominated at the other sites. Our results reveal that high glacial discharge and high ice-scouring frequency influences benthic community structure, resulting in suppressed mineralization rates at glacier fronts. In contrast, intermediate disturbance seem to structure benthic communities in a way that causes higher mineralization rates compared to sites with low disturbances. In conclusion, ongoing warming will cause increasing remineralization rates in Antarctic coastal waters due to warming related increasing disturbance by glacial discharge and ice-scouring and their modifying effect on benthic community structures.