Since European settlement, human activities have degraded many wetland environments. The following lists some activities that threaten the values of wetlands in Western Australia.

Alteration of natural water regimes

This can be caused by activities such as artificial drainage, the extraction of groundwater, the construction of dams and weirs and the loss of vegetation (see below). Plants and animals that inhabit wetlands are often dependent on a particular water regime, and may be affected by changes in water levels and inundation.

Loss of vegetation

The vegetation that occurs around wetlands is an important component of the ecosystem. The vegetation assists in maintaining regular wetland water regimes (see above), provides Habitat and food for fauna, protects against salinity and erosion, provides soil stability, filteres pollutants and provides natural beauty while assisting in the maintenance of a healthy wetland. The loss of vegetation will result in the loss of these values.

Salinisation and Excessive Inundation

Salinisation and excessive inundation are widespread issues in agricultural areas and are generally caused by the replacement of perennial deep rooted native vegetation with shallow rooted introduced annual crops and pasture. Because annual crop and pasture species use less water than native vegetation, this can result in a rise in the water table bringing with it dissolved salts that have accumulated in the surface layers of the soil. A few effects of salinity and excessive inundation on wetlands include a reduction in water quality.  Aquatic invertebrate communities can be affected and permanently altered because some invertebrate have a lower threshold or tolerance of salinity.  Wetland plants that cannot tolerate high levels of salt in the soil or the extended period of inundation can die as a result of these factors. Mining is also a factor that can cause salinisation in wetlands.

Water pollution

The contamination of a water body can be caused by various activities, including the use of chemicals (such as fertilisers and pesticides) in the catchment of wetlands, the drainage of pollutants and toxic materials into wetlands, and accidental chemical/oil spills. Some contaminating substances can be harmful to wildlife and can greatly reduce the water quality of the wetland. The use of fertilisers in the wetlands catchment can cause nutrient enrichment in the wetland. This has the potential to cause algal blooms in the water body. These blooms in turn may be toxic to some fauna, particularly fish and waterbirds, and result in events such as fish kills.

Introduction of invasive species

This includes the introduction of weeds and feral animals (such as carp, mosquito fish, Salvinia, grasses, donkeys, goats and camels) into the wetland environment. Weeds invade and compete with native plant species for resources. Feral animals are known for their destructive impact on wetland areas and can disrupt the intricate food chains that exist within the ecosystem.

Natural processes

Fire, floods, cyclones and drought are all naturally-occurring processes that have the potential to damage wetland environments. Fire can remove and alter habitat available for wildlife around wetlands. Floods, cyclones and drought can impact the natural water regime of the water body and the vegetation surrounding the wetlands.