A biophysical inventory of the Papineau estate was conducted in 1994; it described the natural environment of the property and made recommendations for its preservation. The inventory shows that the historic site is situated in a region where the temperate climate is the mildest in Québec. The bioclimatic domain is that of sugar maple-basswood and sugar maple-hickory groves.
After the last ice age, the Ottawa River was a powerful waterway that played a decisive role in shaping the landscape. As its river bed has remained wide and its flow strong, it has eroded the forms that it had previously shaped, to the extent that on the north shore today we find a stepped landscape: first, flat sandy banks along the river, then pre-Cambrian hills that skirt the valley to the west beginning several hundred metres from the bank.
The rock base of the site is part of a Proterozoic formation composed of marble and calc-silicate rock. An outcrop of this rock is seen on Cape Bonsecours, which is partially covered with glacial till. Around the cape are deposits of sand carried by the present-day river, and marine clay and sand from a glacial river delta located near the town of Montebello. Only unfertile regosols have managed to develop on these relatively recent deposits. Papineau Stream, crosses the site, its mouth located at the eastern end of the estate.
Woodlands cover more than half of the area of the Manoir Papineau National Historic Site of Canada. They are exceptionally diverse if you consider that over an area of several hundred square metres there are four maple groves, a stand of hemlock spruce, a pine forest and two communities of various deciduous species. The woods surrounding Cape Bonsecours is dominated by populations of varying ages. Although the forest is natural, it has not reached an evolutionary equilibrium. It is the result of natural and human disturbances that affected the site over a century ago.
The trees on the national historic site are representative of the ecoregion surrounding it in that no rare woody species are found. In terms of individual species, several specimens of red oak, cottonwood and silver maple have reached a respectable age and size and are in excellent health. The January 1998 ice storm damaged close to 80 percent of the trees to varying degrees. Nevertheless, only several trees had to be removed because of the extent of damage. An inventory of endangered plant species was conducted at the national historic site in 2002 and in the proximity of the funeral chapel a species was found that appears on a list of species that will likely be designated as “endangered or vulnerable” by the Québec department of the environment: the Downy-Rattlesnake plantain (Goodyera pubescens), an orchid typically found in drywood habitats. Two other plants, the Asa Gray sedge and cat-tail sedge, have also been identified; these species are not presently considered to be vulnerable or endangered in Québec, but are very rare.
Human-caused disturbances have been limited to the landscaping elements near the manor, as well as Manor House Road and the network of trails on the site.
Wildlife is not abundant on the site. Its southern location makes it a good environment for animals, but the open nature of the woods limits the quality and quantity of habitats. There are, nevertheless, several bird species that can be observed, as well as some small mammals, such as chipmunks and grey squirrels. Papineau Stream is a potential habitat for fish, amphibians and small reptiles.