Habitat alteration such as the filling of marshes and tidal flats, and reconstruction of shorelines to accommodate the needs of development, transportation, and agriculture, can degrade estuaries. Wetland loss and degradation have limited the amount of habitat available to support healthy populations of wildlife and marine organisms. The clearing of land to obtain timber, the construction of homes and roads, and other development projects completed without properly revegetating the area can lead to excessive sediments being washed into the estuarine environment. These sediments muddy the water, preventing sunlight from reaching aquatic vegetation and making the water unappealing to swimmers. Sediments can also carry excess nutrients, pesticides, and toxic substances, causing additional water quality problems.
Estuaries are vulnerable to the introduction of a wide variety of toxic substances .
Bottom-dwelling organisms like shellfish are exposed to these chemicals and can pose a risk to human health if consumed. Wildlife and aquatic plants and animals can also be harmed through the consumption of contaminated fish and water. Intentional or accidental introduction of invasive species can often result in unexpected ecological, economic, and social impacts on the estuarine environment. Through predation and competition, introduced species have contributed to the loss of some native populations and the drastic reduction of others. Overpopulation of some introduced herbivorous species has resulted in overgrazing of wetland vegetation and degradation and loss of marsh habitat.