The Daintree lowland tropical rainforests are of international importance, as they represent the last areas of tropical lowland forests that were once quite common in the far north of Queensland, but they have largely fallen to the incessant push for agricultural development (most of these forests have been converted into sugar cane fields and some urban development). More importantly, these remaining forests have an almost continuous connection with the upland forests of the coastal range, which is not the case for other fragments.

The region is characterised by a high botanical diversity (over 1700 species of flowering plants) and, in particular, a high diversity of restricted endemic species of plants. Even though much systematic collecting has been done, new species are still being discovered. The region has a high diversity of elements of Malesian origin, such as Syzygium and figs. Refugial areas, mostly valleys extending into the uplands, are all characterised by having a unique assemblage of restricted endemic species associated with each of them. Many endemics (such as Idiospermum australiense) are considered to be relict species from the time preceding the break-up of the Gondwanan super-continent. Some of these relict species are highly restricted in spatial range. One, Noahdendron nicholasii (Hamamelidaceae - the witch-hazel family), is restricted to an area of no more than 20 hectares at Noah Creek.

Despite the high botanical diversity there is not a corresponding high diversity of mammal and bird species, which is presumed to reflect the species losses associated with the expansion and contraction of the rainforests during the Pleistocene period, and with the ecological changes associated with the coming of humans to the continent. Generalists dominate both the mammal and bird fauna. Bats are the predominant mammals with six species of megabats (Pteropodids - flying foxes [fruit bats] and their relatives) and an estimated 20 species of microbats (all insectivorous), followed by rodents.

The area is known as the place where the "rainforest meets the reef," which is particularly true of Cape Tribulation, where there is a continuous sweep of forest from the coastal uplands to the ocean and the fringing reef.