The Antarctic region is usually considered a pristine area. Nevertheless, regional warming effects and increasing human activities, including the presence of several research stations, are inducing considerable environmental changes that may affect the ecosystem’s functions. Therefore, during the XXXIII Antarctic expedition, we carried out an investigation in Terra Nova bay (Ross Sea), close to the Antarctic Specially Protected Area (ASPA) n.161. In particular, we compared the effects of two different types of impacts on the meiobenthic assemblages: anthropogenic impact (AI), associated with the activity of Mario Zucchelli Research Station (MZS), and natural impact (NI) attributable to a large colony of Adélie penguins (Pygoscelis adeliae) in Adelie Cove. For each impacted site, a respective control site and two sampling depths (20 and 50 m) were selected. Several environmental variables (pH, dissolved oxygen, major and minor ions, heavy metals, organic load, and sediment grain size) were measured and analysed, to allow a comprehensive characterization of the sampling areas. According to the criteria defined by Unites States Environmental Protection Agency (US EPA 2009), heavy metal concentrations did not reveal critical conditions. However, both the MZS (AI20) and penguin colony (NI20) sites showed higher heavy metal concentrations, the former due to human activities related to the Italian research station, with the latter caused by the penguins excrements. Meiobenthic richness and abundance values suggested that the worst ecological condition was consistently related to the Adélie penguins colony. Furthermore, the higher contribution of r-strategists corroborates the hypothesis that the chronic impact of the penguin colonies may have stronger effects on the meiobenthos than the human activities at the MZS. Food is not limited in shallow Antarctic bottoms, and microscale differences in primary and secondary production processes can likely explain the greater spatial heterogeneity, highlighted both by the univariate and multivariate attributes of meiobenthic assemblage (i.e., richness, diversity, abundance, whole structure assemblage, and rare taxa) at the deeper stations. As reported in other geographical regions, the assemblage structure of rare meiobenthic taxa is confirmed to be more susceptible to environmental variations, rather than the whole assemblage structure.