Fire
Uncontrolled wildfires have become an increasingly serious threat to native ecosystems in the TMA area. Wildfires leave the landscape bare and vulnerable to erosion and non-native weed invasions. Invasive weeds, particularly fountain grass (Pennisetum setaceum) which is a fire-adapted weed that has evolved to rely on fire for regeneration, are quick to reclaim burned areas, further changing the natural fire dynamics.
Hoofed animals, or ungulates
Pigs, goats, mouflon, sheep, and cattle are a major threat to the TMA area. Wild (feral) ungulates destroy native vegetation and prevent its regeneration through consumption, while accelerating the invasion of weed species through direct dispersal of seeds on their coats and in their droppings. In addition, pig wallows provide mosquito-breeding habitat that promotes the spread of avian malaria and pox – the two most deadly diseases for native forest birds, as well as human diseases. In some landscapes, feral ungulates have caused severe and extensive erosion, directly affecting both the forested uplands and the nearshore coral reefs. Cumulatively, ungulate impacts cause the decline of intact native ecosystems which can affect watershed functions and jeopardize the future existence of rare and endangered plants and animals.

Weeds
One of the major threats to native ecosystems and species in the TMA area is the uncontrolled spread of invasive non-native plants. These plants displace distinctive native flora, resulting in a loss of species diversity and eventually in more pronounced and permanent changes to ecosystem function such as alteration of primary productivity and nutrient cycling. Many invasive species completely replace native vegetation resulting in total loss of native habitats.
Small animals
Smaller animals also have the potential to become serious pests in the watershed. Feral cats, rats, mongoose, dogs, house mice, and certain non-native birds are known to consume or compete with native species. In addition, like ungulates, small mammals can affect water quality by serving as vectors of water-borne diseases.
Other threats include introduced diseases and pathogens, human disturbance, and climate change.