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Estuaries, or transitional waters, represent the transition between freshwater and marine environments and are influenced by both aquatic realms. Salinity level marks the position within the mixing zones of an estuary. The uppermost limit of an estuary is referred to as its head, while the southernmost limit is called the mouth of the estuary. Between the freshwater head and the saline mouth of the estuary lie a number of zones marked by intermediate salinity values, each with distinct characteristics pertaining to the water clarity and type of substratum, thus hosting different communities of organisms.

Division of transitional waters (Carricker, 1967[1]; McLusky, 1989[2])

The challenges of estuarine ecosystems

Estuaries are very peculiar yet challenging ecosystems. The main challenge and at the same time the most important feature governing species diversity of transitional waters is the variable salinity regime. Salt dissolved in water applies what is called osmotic pressure on the cell walls of living organisms, dehydrating it. Organisms living in saline media such as the sea water are equipped with buffering mechanisms allowing them to retain their body fluids in the presence of salt. In most cases this mechanism is adjusted to a particular dissolved salt level and yields a distinction between freshwater and marine species, into which most organisms of aquatic life fall. In turn very few species can withstand variable salinity, which has implications for the biodiversity of estuaries.

Turbid waters of the Shannon Estuary

Lowland reaches of rivers are characterised by high levels of suspended solids, such as silt and organic detritus, inducing high turbidity (water cloudiness). When the water carried with a river collides with the seawater, these particles become effectively ‘trapped’ (Kranck, 1981[3]). Estuaries are naturally turbid environments and among the factors shaping the diversity of estuaries particulate matter claims much of the relevance (Robinson et al., 1999[4]). In many estuaries and tidal channels particles are trapped at specific locations due to converging suspended sediment fluxes. These convergences result in pronounced estuarine turbidity maxima (ETM) and the majority of primary production in estuaries occurs on the seaward side of the ETM (Swart, 2007[5]).

Turbidity limits the depth of photic zone (light penetration zone), thus limiting the photosynthesis and primary production. Macrophyte vegetation and benthic algae are often limited to the periodically exposed (intertidal) part of the estuary, while the growth of phytoplankton is restricted to a thin uppermost layer of the water column (Cloern, 1997[6].) As a result, estuaries are heterotrophic systems, where more energy is consumed than produced. Most estuarine species are detritivores, meeting their energy intake requirements from organic matter contained either in the sediment (deposit feeders), in suspension (filter feeders) or both and benthic invertebrates play a major role in energy transfer and circulation in estuaries (Wilson & Parkes, 1998[7]).

The particulate matter eventually settles out and the substratum of estuarine mid reaches tends to be composed of fine fractions, typically creating extensive sand and mudflats. These conditions hinder organisms with an affinity for hard substratum but constitute important habitats for a range of burrowing invertebrate species, of which bivalve molluscs and polychaete worms are usually dominant in terms of numbers and biomass. These in turn provide a rich feeding opportunity for a range of higher consumers.

Industrialised and urbanised river catchments and estuaries receive anthropogenic input from various sources, both point and diffuse and often carry a range of contaminants. Sheltered, low-energy areas such as intertidal mudflats in enclosed bays or estuaries are most susceptible to these pollutants as dispersion is low and the finer substrata in these areas act as a sink for contaminants making estuarine benthic fauna susceptible to pollution (Kausch & Michaelis, 1996[8]).

Biodiversity of estuarine ecosystems

Species richness in estuaries follows a long established pattern along the salinity gradient described by Remane (1934[9])

Truly estuarine species are those that complete their whole life cycle within the transitional waters. Those permanently dwelling there are mostly hardy, stress-tolerant species able to handle salinity shifts and high suspended solid levels. Not many species can perform well under such conditions thus the estuarine ecosystems are typically characterised by relatively low species diversity comparing to freshwater or full salinity conditions. Freshwater species are becoming less abundant with increasing salinity and are gradually replaced by marine organisms moving down the estuary with some truly estuarine species found at intermediate salinities. This pattern is reflected by the overall species richness, where the least diverse fauna is found at salinity levels of between 5 and 18 PSU.

Apart form the permanent dwellers, estuaries play host to a number of visitors. Some of them have to travel through estuaries on their migratory route, being either anadromous (spawn in freshwater and feed and grow at sea) or catadromous (spawn at sea and feed and grow in freshwater). The absence of many of the marine predators and rich particulate food supply is what offers attractive spawning and nursery grounds for many species that normally live under full salinity conditions. Even though estuarine ecosystems are usually species-poor, they maintain a high productive throughput of invertebrate fauna. This productivity provides rich feeding opportunities for a range of higher consumers. Some marine predators are well equipped to cope with reduced salinity and frequently penetrate the estuaries in search of food. In turn, retreating tides make the estuarine beds available to terrestrial predators, of which birds take the greatest share. Estuarine sand and mudflats that are periodically exposed to air support a variety of bird fauna in high densities. This value of estuaries has been long recognized and many estuarine sand and mudflats have been designated as Special Protection Areas (SPA) under the EU Birds Directive (79/409/EEC).


Estuarine ecosystems are ususally dominated by stress-tolerant organism, able to whithstand a relatively wide range of environmental fectors. However they to face some threats from anthropogenic activities.

  • Certain aspects of estuaries such as their high productivity and availability of a natural interconnectors between maritime and inland waterways make them desirable lactions for human settlements. Residential, recreational and industrial developments (such as marinas, harbours or ports) are usually located right at the waterfront with supporting structures such as embankment impacting on the upper shore communities. Estuaries are often challenged by land development and land reclamation is particularly detrimental in this respect as it results in a permanent loss of habitat.
Highly polluted and channeled section of the Liffey Estuary.
  • Rivers discharging into their estuaries carry various constituents resembling the landuse of the drainage area (catchment). This means that various contaminants introduced at any point in the catchment ultimately end up in the estuary. Although estuarine organisms are typically hardy, these pollutants and excess nutrients impede their overall performance (including growth and reproduction) and in densely populated or heavily industralised catchments pollution can have detrimental effects on life in estuaries.
  • Main aspects of climate change of concern for the estuaries is the overall temperature rise and elevation of the sea level. The first one is likely to induce latitudinal migration with more warm-water species being increasingly established and possibly outcompeting the native species in a long run. The sea level rise would result in a shift of the salinity zonation landwards. However, coastal areas, including estuaries, are usually heavily populated and developed. In such developed areas the vertical shift of salinity zonation can be hindered by flood defence structures and river and shore embankments resulting in estuarine squeeze.

Further reading


  1. Carriker, M. R. (1967). Ecology of estuarine benthic invertebrates: a perspective, p. 442-487. In G. H. Lauff (ed.), Estuaries, American Association for the Advancement of Science. Washington.
  2. McLusky, D. S. (1989). The Estuarine Ecosystem, 2nd Ed. Chapman & Hall, London.
  3. Kranck, K. (1981). Particulate matter grain-size characteristics and flocculation in a partially mixed estuary. Sedimentology 28: 107 – 114.
  4. Robinson M. C., Morris, K. P. & Dyer, K. R. (1999). Deriving fluxes of suspended particulate matter in the Humber Estuary, UK, using airborne remote sensing. Marine Pollution Bulletin, 37: 155 -163.
  5. Swart, de H. E., Schuttelaars, H. M. & Talke, S. A. (2007). A simple model for phytoplankton growth in turbid estuaries. Geophysical Research Abstracts 9, 04190.
  6. Cloern, J.E. (1997). Turbidity as a control on phytoplankton biomass and productivity in estuaries. Continentla Shelf Research 7: 1367-1381.
  7. Wilson, J.G. & Parkes, A. (1998). Network analysis of the energy flow through the Dublin Bay ecosystem. Biology And Environment: Proceedings Of The Royal Irish Academy 98B (3): 179–190.
  8. Kausch, H. & Michaelis, W. (eds.) (1996). Suspended particulate matter in rivers and estuaries - Proceedings of an International Symposium held at Reinbek near Hamburg, Germany. Advances in Limnology, 47.
  9. Remane, A. (1934). Die Brackwasserfauna. Verzeichnis der Veröffentlichungen Goldsteins, 36: 34–74. .

The main author of this article is Penk, Marcin
Please note that others may also have edited the contents of this article.

Citation: Penk, Marcin (2009): Estuaries. Available from [accessed on 18-08-2017]