“The Gully”, situated off Nova Scotia, Canada, is the largest submarine canyon in the western North Atlantic. This unique oceanographic feature, which became a Marine Protected Area (MPA) in 2004, is rich in marine biodiversity and is part of the critical habitat of Endangered northern bottlenose whales (Hyperoodon ampullatus). To understand the potential impact of plastic pollution in the MPA and on this Endangered cetacean, we evaluated trends over time in the abundance and composition of plastics and compared these to the stomach contents of recently stranded northern bottlenose whales. From the 1990s–2010s, the median abundance of micro-sized (<5 mm) and small plastics (5 mm–2.5 cm) increased significantly, while the median abundance of large plastics (>2.5 cm) decreased significantly. Plastic abundance from the 2010s for micro-sized and small plastics varied from 5586–438 196 particles km−2, higher than previously measured estimates for surrounding offshore areas. Polymers identified using FTIR spectroscopy included polyethylene, polypropylene, polyethylene terephthalate polyester, nylon, alkyds (paint), and natural and semi-synthetic cellulosic fibers. The abundance of large debris ranged from 0 to 108.6 items km−2 and consisted of plastic sheets and bags, food wrappers and containers, rope, fishing buoys, and small plastic fragments. Whale stomach contents contained fragments of fishing nets, ropes, bottle caps, cups, food wrappers, smaller plastic fragments, fibers, and paint flakes, consistent with the composition and character of items collected from their critical habitat. Despite being far from centres of human population, the unique oceanographic features of The Gully (i.e. currents and bathymetric complexity) may concentrate plastic debris, increasing exposure rates of whales to plastic pollution. The increase in micro-sized and small plastics over time suggests associated health and welfare impacts of ingested plastics should be accounted for in future recovery plans for this Endangered species.