Because of the complex topography and oceanography within the monument, and the resulting high food production, there is a rich diversity of fishes. Scientists consider the Monument a biodiversity hotspot for deep-sea fishes.

In a 2003 study, 591 fish species were found living below 650 feet in the New England shelf region of the monument. Expeditions to Bear Seamount found several rare fish species that were previously unknown to occur in this area of the Atlantic Ocean. The canyons are home to various species of flounders, hake, skates, ocean pout, cusk, grenadiers, and eel; some of which occur in dense aggregations.

Larger pelagic fish like swordfish, tuna, and sharks also use the monument. In fact, many shark species rely on the coral ecosystems found within the monument for the beginning of their life cycle, with egg cases being deposited on the corals.