The loss of coastal fish habitat is one outcome of nitrogen pollution. Similarly, soil erosion and desertification cause loss of habitat, as trees and bushes which were once home to many beings become incapable of supporting much life at all. Then there is the habitat loss more directly caused by agriculture: the replacement of certain native/indigenous ecosystems with agriculture.
Usually, as mentioned in the intro, this agriculture is a monocultural one. In the tropics, sugarcane, bananas, coffee, and pineapples are examples of monocultures that have historically (and still!) displaced abundantly productive and biodiverse native ecosystems. In temperate climates, the major crop culprits are grains, like corn and wheat, but also soy, cotton, and other monocropped vegetables. Grazing animals have also been linked to forest clearing. The world over, wherever humans have created large-scale intensive farming systems, destruction of habitat has led to a reduction in species counts and species diversity.
Certainly, smaller scale production has displaced habitat, as in the “slash and burn” techniques that many tropical climate peoples have used to create sunnier spaces amidst deeply shaded rainforests, in order to plant and harvest sun-demanding crops. The difference is that many of these historic forms of habitat destruction were (1) temporary, in that they were part of shifting cultivation systems that moved around and thus allowed the once burned and planted plots time to recover, and (2) small, and therefore not destroying entire regions of habitat. Many large animals or birds, for example, will survive fine losing 10 square meters of forest here and there, but will suffer major hardships when square kilometers of their habitat are cleared at once.
The latter kind of habitat destruction occurs in industrial-style and scale plantations. One of the worst culprits of the past 15 years is palm oil, the expansion of which has contributed to the near extinction of the Pygmy Elephant and the Orangutan. Palm oil plantations are huge and long lasting—and need to be so in order to provide sufficient profits for their creators. This shows another distinction between typical small- and large-scale habitat disruption: the former motivated by subsistence needs, the latter motivated by greed for profits.
The elephant and orangutan are (perhaps) only the most charismatic of animals and plants endangered by habitat destruction: around the world, loss of habitat (which is partly an urbanization issue but is mostly driven by agriculture) has led to what scientists are calling the “6th Great Extinction”. Species of all sorts are dying out or becoming incredibly rare—and whereas the first five great extinctions were related to major geologic events (huge volcano eruptions, meteors falling to earth), this will be the first caused by human activity.
Habitat loss is happening both on land and in the sea. On land, the clearing of forests, urbanization, and draining and damming of natural water bodies all have led to land and water habitat loss. A horrifying example is the Aral Sea in Eurasia: once the largest terrestrial lake (bigger than the U.S.’s Lake Superior), the Sea has practically disappeared—in the course of only 30 years! Simple diversion of water for agriculture has been the major cause of its disappearance, which has affected untold numbers of species who relied on its waters and the food it once produced.
The oceans are also changing for the worse. Corals are dying from (among other factors) changes in ocean temperatures due to climate change. Ocean acidification is also a result of climate change, with uncertain but likely disastrous results. Industrial fishing companies who literally drag nets along the seafloor are destroying seafloor habitats, while killing creatures that the nets are not even intended to catch.
Simply, humans have prioritized our own needs above those of other species, to the point where we might even be compromising our own future survival, as we destroy habitats and species vital to our own survival. For a sustainable future—not to mention for ethical reasons—this has to change.
 This is the theory that underlies the argument of the fantastic book “Nature’s Matrix”—It’s likely I’ll be referring to this book repeatedly.