Microplastic particles (<5 mm) have been observed to be widely distributed in the oceans, from estuaries the deep ocean trenches. While plastic pollution in the marine environment is a growing concern worldwide, relatively little is known about microplastic distribution and accumulation on the seafloor, particularly in marine protected area (MPAs). The delimitation of MPAs frequently follow jurisdictional or political boundaries, however the distribution of species, habitats and ecosystems does not always follow these same confines. Likewise, pollution in the marine environment do not have boundaries. This study compares microplastic content in sediment cores from two sites: an urbanised area, near the coastal township of Picton; and a site distal from the township (∼30 km) but proximal to open ocean, adjacent to the Kokomohua Marine Reserve, in the region of Queen Charlotte Sound/Tōtaranui (QCS), Aotearoa/New Zealand. Microplastic particles were identified throughout the sediment cores from both locations, reaching depths of ∼45 cm below the seabed. Our findings revealed that marine sediments adjacent to the marine reserve had four times the microplastic accumulation of marine sediments from near the coastal township. The abundance of microplastics across the sediment depth profiles also varied between the two sites, suggesting different accumulation of microplastics on the seafloor due to differences in the frequency and extent of seabed disturbance experienced by the two locations. Our study demonstrates the extent to which human stressors such as microplastic pollution proliferate and concentrate in the environment, particularly in areas considered to be near-pristine with strict environmental protections.