This study shines a light on the challenges faced when investigating microplastics in perceived “pristine” regions. Sharing results from samples taken using a hydrobios Microplastics sampling net from the surface waters in the Atlantic portion of the Sub-Antarctic to the Antarctic Peninsula. This region is home to some of the highest concentrations of zooplankton biomass but is also threatened by increasing shipping traffic from fishing and the growing tourism market. It was found that 45.6% of the plastic particles isolated from seawater samples were sampling contamination, originating predominantly from the ship. Whilst we found that micro and mesoplastic concentrations in seawater were significantly low (0.013 ± 0.005n/m³) compared to global averages, they were higher along the Antarctic Peninsula than the open ocean (Sub-Antarctic) stations. The potential availability of micro and mesoplastics to pelagic amphipods was explored, using an observed encounter rate (OER) and a possible encounter rate (PER). The total OER (0.8%) was higher than the PER (0.15%), suggesting that even at low concentrations, microplastics are encountered, and potentially consumed, by amphipods. This study highlights the need to prioritise regions of high zooplankton abundance and to investigate both water and biota to build up a picture of plastic pollution and its potential interaction with the Antarctic Ecosystem.