Antarctic marine ecosystems are largely thought to be among the planet’s least impacted, yet habitats adjacent to research stations can be heavily polluted. Despite long-term monitoring and remediation being high priorities for international environmental protection, the ecological responses to contaminants and stressors remains poorly characterised, limiting our ability to manage and reduce human impacts. This study compares epifaunal community composition at two sites close to Scott Base with a reference site further away. We couple these data with environmental characteristics, including current data, sediment properties, and contaminant concentrations within the sediment and in the tissues of two epifaunal species, both from this survey and those previously reported. Previously high concentrations of polychlorinated biphenyls and polyaromatic hydrocarbons are now undetectable and concentrations of heavy metals were mostly similar or reduced compared to previous data from 2002. High within-site variance suggests localised contamination footprints from being situated within a deposition zone and/or from the erosion of anthropogenic debris. Despite the persistence of some metals (arsenic, copper and lead) at one site, our study revealed high biodiversity at all three sites (22–28 taxa per 0.25 m2). Benthic community structure was influenced by a combination of factors, including sea ice characteristics, sediment type and habitat complexity. Overall, our study clearly highlights the influence of human activities on the benthos in adjacent marine habitats. The established monitoring protocols coupling diver and remote sampling will enable regular monitoring, filling a critical need for time-series data in order to detect long-term trends and interactions with climate drivers.