The combination of a persistent high-energy environment, the overlap of tropical and temperate fauna, and the influence of the Leeuwin Current supports extensive seagrass meadows and benthic communities, providing critical habitat for species such as pink snapper, mulloway, herring, dhufish, and grouper. The reef is recognised as an area of ecological significance for its rare and endangered marine mammal and seabird assemblages. It is categorised as a biologically important area for whales (pygmy blue, southern right and humpback) and seabirds (wedge-tailed shearwater, fairy tern, bridled tern, little shearwater and flesh-footed shearwater).

The Bouvard reefs are an offshore submerged Tamala limestone ridge. The Bouvard Reefs are the southern extension of the ridge of the Five Fathom Bank. Behind Myalup and Preston beaches, continuous blowouts and parabolic dunes average about 1 km in width, expanding to 2–3 km near Yalgorup and Cape Bouvard. To the north, the Holocene dunes overlap an inner Pleistocene barrier. This barrier consists of three shore-parallel Pleistocene dune systems, separated by wetlands and lakes, including Lake Preston and Lake Clifton.

The Noongar People are the native title claimants for south-west Western Australia. They have also agreed an Indigenous Cultural Heritage Land Use Agreement (ILUA) between the state of Western Australia and the Gnaala Karla Booja people within the larger Noongar native title area. This agreement covers the sea within a 3 nautical mile limit. The indigenous group of Bouvard used marine resources including spearing of seals and camped along the coast to fish; the reef was an important feature to their livelihood. Additionally, there are a number of fish traps known along the coastline.