Restoring estuarine ecosystems

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Ecological value of estuaries

Estuaries are located on the transition between the freshwater and marine environments. As a result, estuaries are subjected to influences from both: the conditions in the estuaries change under influence of the tides, wave action and freshwater discharge from rivers. This makes estuaries a highly dynamic environment in which salinity and water levels vary in space and time. In response to the dynamic conditions estuaries contain a unique species assemblage.

Estuaries offer suitable habitats for both marine and freshwater species, but also contain species adapted to brackish conditions. The rich species assemblage is also enhanced by the generally high availability of organic matter and nutrients as a result of the hydrodynamic conditions in estuaries and their position downstream from rivers.

Estuarine ecosystems provide important habitat for various fauna species groups. To improve or restore the health of an estuarine ecosystem, it is important to bring back natural dynamics and provide the functions from which the different animals can benefit. Below some examples for fish and bird species are given:


For fish, habitat functions are primarily:

  • shelter: the varying degree of conditions and of vegetation allows species to hide from predators;
  • nursery: many fish rely on the estuarine ecosystem for their species survival. Mating and spawning often occurs in these areas. The vegetation provides suitable substrate for egg deposition. Additionally, estuarine systems are a nursery ground for species, as their reproduction occurs under brackish conditions. For species like plaice (Pleuronectes platessa), flounder (Platichthys flesus) and common dab (Limanda limanda), the Rotterdam harbour is an important mating and reproduction habitat (Kruitwagen and van Deelen 2019);
  • transition zone: some fish species migrate between fresh- and saltwater (diadromous fish). To be able to make this transition, the fish need to adapt to the new salinity conditions. This transition occurs in brackish water. If a stable salinity gradient is unavailable, fish are not able to migrate between salt and freshwater systems. Estuarine systems play therefore an important role in the completion of the life cycle of diadromous species.


For birds, the estuarine ecosystem provides:

  • food: Wader birds, for example, feed on mudflats which fall dry during low tide. Every species of wader birds has their niche during the tidal cycle in which they forage for food, where the different species move forward as the tide line slowly retracts. A gradual slope of the shore thus creates the longest foraging time for the birds, allowing for more individuals to feed on the mudflat;
  • high water refuge: these are islands which emerge during high tide. While many birds feed during low tide, they need a save refuge during high water. These areas should not be accessible for terrestrial predators.
  • resting zone: for migration birds, the estuarine ecosystem is an ideal resting stop. It can provide sufficient food and the birds can rest on high water refuges.

Due to (anthropogenic) changes, the function of estuarine ecosystems has degraded worldwide, causing a significant decrease in fish populations and habitats for birds (Deinet et al. 2020) . This page provides further insights into important processes and parameters for the ecological functioning of estuaries. The understanding of these processes can aid in improving the health of ecosystems, which is explained on the ‘how to’ page.

Abiotic conditions

The degree to which estuaries present valuable habitat to species is closely connected to the abiotic conditions within the estuary. Important abiotic conditions that define habitat suitability include:

  • salinity;
  • water level;
  • hydrodynamics and morphology;
  • water quality and nutrient dynamics;

Strengthening and/or restoration of ecological functions requires that the abiotic conditions and related physical processes are taken into account. If this is done properly, the biology and ecology will follow. The most well-balanced, resilient ecosystem will emerge when the physical processes closely resemble a natural state.


Salinity tolerance

Salinity is one of the dominant factors in determining the habitat suitability in an estuarine environment. The salinity describes the concentration of salt in the water. The physiology of species determines their salinity tolerance. This tolerance depends on the salt concentration in the water and the salt concentration in the body tissues of species. When there is a difference between both concentrations, chemical processes are aimed at restoring the equilibrium through osmosis. Marine species are adapted to this situation by having high salt concentrations in their tissues. In contrast, freshwater has a low salt concentration. Correspondingly freshwater species generally have low salt concentrations in their body tissues.

The physiology of both marine and freshwater species is adapted to the prevailing salinity concentrations in their environment. This adaptation presents challenges when species move to an environment with a different environment. If a marine species moves to freshwater, osmosis will attempt to restore the balance in the salt concentrations in the water and in the organism, leading to the uptake of water in the body tissues in an attempt to dilute the salts. If a freshwater species is placed in the marine environment, water is drawn from the body tissues by osmosis to restore equilibrium. In both cases, the species will experience stress. In most species the physiological ability to adapt to a different salinity concentration is limited. The diadromous species, species that spend part of their lifecycle in freshwater and part in seawater, are best adapted. But even these species require time for physiological adaptation.

As a result of the physiological challenges connected to salt, the species diversity in the estuarine environment is closely connected to the salinity and the dynamics in the salinity. Few species are able to thrive in environments with rapidly changing salinity. This illustrated for the fish communities in the Baltic Sea by the Curve of Remane (see figure) (Whitfield et al. 2011). Only a small percentage of species are able to thrive in brackish conditions.

Conceptual model for estuarine biodiversity (species) changes covering the salinity continuum from fresh-water (oligohaline) to salt (hypersaline) conditions (Curve of Remane, adapted) source: (Whitfield et al. 2011)

Salinity gradient

Another determining physical process in an estuarine ecosystem is the salinity gradient. With the tidal influence as a driving force, saltwater and a varying degree of freshwater flow in from rivers, create a salinity gradient. Salinity levels slowly decrease from >35‰ in the sea to <5‰ in the rivers. In estuaries, a gradient in salinity is observed due to the mixing of freshwater and seawater. Over this gradient, the salinity gradually increases in the direction of the sea. The range over which the mixing occurs is not fixed and moves depending on river discharge and the strength of the tidal flow. During high tide and with low river influx, there is more salt intrusion than during low tide and with high river discharge.

Due to a difference in salinity tolerance, the salinity gradient translates into differences in spatial distribution of species in both flora and fauna. For instance, one can expect macroalgae (such as seaweeds) under salt or brackish conditions. As the salinity drops, water plants, such as halophytes, may emerge. Because salinity may change over time due to variations in river discharge and tidal force, the spatial distribution of most species corresponds to the extremes in salinity that occur.

The density of saltwater and freshwater is not the same. As a result, vertical stratification may occur (isohalines). Stratification is many determined by (Geyer and MacCready 2014):

  •  water depth;
  •  vertical mixing by tidal currents;
  •  river discharge.

The combination of these factors determines whether a system is well-mixed, periodically-, weakly- or strongly stratified. This stratification can limit the exchange of nutrients and suspended matter between the salt- and freshwater layer. Vertical stratification has a range of biological effects, both direct and indirect. This results in a complex relationship with the local ecology (Jassby et al. 1995). As a result of stratification marine and freshwater species can be present in different layers of the water column at the same geographical location, resulting in a highly diverse species assemblage.

Schematic overview of the salinity gradient and mixing (Maccready and Geyer 2009). White lines indicate the isohalines and the arrows show the strength and direction of the currents.

Water level

Changes in water level

A clear determining physical process in estuarine ecosystems is that water levels can be highly dynamic. Water levels are subject to:

  • tidal influences: depending on the geographical location and the alignment of the sun and the moon, the tidal range fluctuates. Every 2 weeks during new and full moon and full moon a spring tide occurs, when the tidal range is largest. During neap tide, the tidal range is smallest.  Depending on the geographical location tidal ranges can vary between decimetres up to many metres;
  • river discharge: with the melting of snow or ice upstream or increased rainfall (tropical wet season), the inflow of river discharge can increase substantially. This (seasonal) effect can be strongly influenced by human interference. In the Netherlands for example, locks and pumps control the outflow of water. As a result, river water levels may be elevated up to several meters for a period of a few weeks;
  • metrological changes: as a result of wind set-up, the water level can vary. This can lead to a set-down or set-up in water level in an estuary.

Ecological significance of variation in water level

Water level variability, and their recurrence interval, are an important factors in determining the spatial distribution of species in estuaries. The variations result in species distribution patterns that follow elevation levels. This can particularly be observed in sessile (non-moving) species. The variation in water level influences the area of the intertidal zone where plants (freshwater) or seaweed and shellfish (saltwater) are present. The effect of the high tide and low tide on the vegetation in a freshwater tidal area is indicated in the figure below. As a result, a clear zonation of embankment vegetation can be found. The zonation in sessile and semi-mobile species largely reflects the extremes in water level that occur.

Effect of tidal range on the vegetation zones of tidal area close to the sea (upper figure) and more up-stream (bottom figure).

Hydrodynamics and morphology

Hydrodynamics are key processes that shape the morphology of estuaries. Hydrodynamics describe the water movements. These water movements influence sediment transport. The hydrodynamics and morphology together give a base for the estuarine habitats and therefore strongly influence the working of the ecosystem.

Tidal flow can bring in sediment from the sea, while rivers bring in sediment from the landward boundary. Under perfectly sinusoidal tide, sediment would move approximately the same distance in landward direction during high tide as in seaward direction during ebb. It is therefore the difference in peak ebb and peak flood currents and the duration of those phases that determines the net sediment transport direction. More information about this so-called ‘tidal asymmetry’ can be found on the page about strategically placing of fine sediment. Flow conditions also determine the type of material that can be transported (e.g. sand or mud) and whether the sediment can settle (i.e. whether sedimentation takes place). Generally, there is a transition zone between sand and mud deposits in estuaries. Sand settles directly when flow velocities drop while fine sediments are transported a bit further and generally deposit in the most sheltered areas of the estuary.

As a result of human interference, hydrodynamics in many estuaries worldwide have been changed. Resulting in changes in morphology, changes in erosion and sedimentation patterns, and often a loss of habitats. An example of this is the Eastern Scheldt storm surge barrier. This storm surge barrier was the first of its kind ever implemented in a tidal inlet. An inevitable effect of such a structure is constriction of the flow-conveying cross-sectional area of the inlet. This constriction caused a decrease in tidal prism (total volume of water flowing per tidal cycle) into the basin, which resulted in a sharp decrease in sediment transport capacity and filling in of the system.

Water quality and nutrient dynamics

The fourth important factor is nutrient availability and water quality (light penetration and oxygen concentration).

The different water flows, both from sea and from the river, provide the estuarine system with nutrients. These provide a source for the estuarine food web. As a result of the import of nutrients and organic matter, estuaries are often very productive ecosystems. Mangroves, for example, rank amongst the most productive ecosystems on earth.

The high load of organic matter and nutrients can also have drawbacks. Excessive loading may result in deterioration of the water quality. Single-cell algae (microalgae) are better adapted to make use of high nutrient conditions than water plants. Under high nutrient conditions, the algae density thus increases. This in turn increases the turbidity of the water. As a result, less light is able to penetrate to the depths where water plants occur. With the plants unable to grow, and unable to take up any nutrients, a positive feedback loop emerges. The algae density increases further and the transparency of the water decreases further, deteriorating the health of the ecosystem. 

The dissolved oxygen concentration affects the flora and fauna as well. If the dissolved oxygen concentration is too low, flora and fauna die. A shortage of oxygen occurs especially at places with high water depth in combination with a low refreshment rate (e.g. docks, basins) or in places with extreme high turbidity. This is a result of underlying physicochemical processes at the sediment-water interface. Particularly in the estuarine environment, anoxic conditions in the sediments are of relevance, both for water quality and for habitat suitability.