Estuaries are the interface between land and sea: semi-closed regions where salt and freshwater mix, leading to a unique community of plants and animals.  An estuary can take many forms that are primarily dependent on its mode of formation( rising sea level, tectonic activity, receding glaciers, or shifting substrate) and water circulation ( tidal influence, topography, and freshwater out flow). However, high productivity, sediment deposition, varying salinity, and high biodiversity are a few traits most estuaries share. In certain areas, such as southern California,  some estuaries may also be referred to as lagoons or bays because low annual rainfall brings in very little freshwater input. 

Estuaries can be subdivided into further habitat types: shallow subtidal, tidal sand or mudflats, salt march, tidal creeks, and the upland transition zone.  Shallow subtidal habitats are submerged but are rarely deeper than light penetration. Mudflats are intertidal habitats that do not support any vascular vegetation. Salt marshes are tidally flushed low lying areas, bordering the estuary supporting salt tolerant plant species. Tidal creeks are streams driven by tidal flow. These areas are usually slow moving and further protected from physical forces. The upland transition zone, also known as riparian habitat, is where the aquatic and terrestrial habitats merge.

Along the West Coast, the Pacific Fishery Management Council identified estuaries as a Habitat Area of Particular Concern (HAPC).

Biological Importance

Varying salinity, tides, freshwater outflow, and water chemistry make very dynamic systems. Because of these conditions, many organisms have adapted in different ways to exploit the environment, leading to a high level of biodiversity. The semi-enclosed nature of most estuaries protects them from wave action and strong currents. Calmer waters allow sediments from freshwater input to settle out, before reaching the ocean, therefore increasing water clarity further out to sea. Typically associated with these sediments in developed watersheds, are high nutrient levels that can be absorbed by many of the estuarine plants, thus reducing eutrophication (higher concentrations of nutrient levels). Estuaries area also vital habitats for marine fishes that use the shallow protected habitat as rearing zones for juveniles. Without these habitat, juveniles would be exposed to physical forces beyond their swimming capabilities as well as high predatory pressure from lack of shelter. The nutrient input, calm waters, and sedimentation of estuaries, allow many plant species to thrive, forming the base of a very productive ecosystem that influences many habitats and species beyond its borders.

Economic Importance

The calmer waters of an estuary provide an ideal setting for aquatic recreation. Many people swim, boat, fish, and hike in or along estuaries every year, providing support for local economies. Estuaries are also readily accessible by the public and can be used for educational purposes.

The nutrient filtering ability of estuaries can decrease eutrophication (higher concentrations of nutrient levels) in coastal waters, protecting other commercially valuable habitats from degradation. Many fishes, such as salmon, use estuaries as a nursery area before leaving for the open ocean. Loss of estuarine habitat would lead to a drop in recreational fishing success. Commercial catches would also suffer, triggering a financial fallout as well as a depletion of an important food source. Because of the high productive of estuarine habitats they can serve as a sink for carbon dioxide, a greenhouse gas responsible for global warming.


Anything that enters into river, flows to an estuary. These inputs may include sewage, urban runoff, and pesticides from urban and suburban area.  Inputs like these, can have acute and chromic effects on the estuarine biota. Estuaries are also vulnerable to increased sedimentation resulting from coastal land development, dredging projects, and reduction in riparian habitat. Excessive sedimentation can fill the estuary, impede tidal circulation, smother plants and animals, decrease water clarity, and reduce the daily change in water volume from tidal flow. Elevated nutrient levels from inorganic and organic fertilizers can cause algal blooms, some of them toxic.  When the nutrients run out, the algae sink to the bottom where they decompose. The bacteria responsible for decompositions remove oxygen from the water, making anoxic zones uninhabitable for many fishes and invertebrates.

Human modification can also harm estuaries. Construction on or around an estuary can disturb or eliminate this important habitat. For example, in California, 90% of its original wetlands have been lost from habitat destruction mainly spurred by a booming population and economic development.