The increasing demand for marine products enhance the pressure on the aquaculture sector and, consequently, on the marine environment. Although shellfish farming does not require additional feeding, it alters the characteristics of the water column and affects marine sediment and benthic organisms through the process of biodeposition of organic material. Meiofauna, a microscopic community inhabiting sediment, serves as a reliable bioindicator of environmental conditions and anthropogenic impact on the marine ecosystem. The aim of this study was to determine the changes in meiofaunal community structure under the influence of mussel farm (Mytilus galloprovincialis). Sediment samples were taken at three stations during the summer period in Novigrad Sea: on the farm’s edge (i.e., P1), directly beneath the farm (i.e., P2), and control station (i.e., CTRL) located approximately 700 meters away from the farm. Triplicate samples were collected through autonomous diving, and a multiparametric sonde was used to record physico-chemical parameters of the water column. The results of our study showed significant variation in total meiofaunal abundance among the sampled stations. The lowest values were recorded at the CTRL station, while the highest abundance was observed at P2, which is associated with the deposition of organic matter. Biodiversity was the highest at the CTRL station, with differences observed only between P1 and CTRL ST. The most abundant taxa at all three stations were Nematodes, Copepods, and Nauplii, with Nematodes dominating and increasing in abundance toward P2, whereas Copepod numbers decreased. However, no differences were found in the number of rare taxa within the study area. These findings indicate a minor, localized impact on meiofauna abundance and community composition. While the total meiofauna abundance increased in area directly beneath the mussel farm, a slight difference in biodiversity was recorded only between the control station and the station on the farm’s edge instalation.