Salinity is a major factor determining the distribution and composition of communities of marine organisms and variations in the salinity regime in estuaries are a characteristic feature defining these systems. The principal factors governing the temporal and spatial nature of the salinity regime in estuaries are the diurnal incursion of the tide and freshwater flow from the river(s). Any activity changing either of these factors can result in a change to the salinity regime.

Potential activities could include physical barriers to tidal incursions, including power generation (tidal) or amenity barrages (e.g. Cardiff Bay) or the consequences of flood defence works on longshore drift of sediment affecting natural bars or spits and physical barriers to freshwater discharge to estuaries such as weirs or other flood defence structures. Many estuaries have obstructions on either the main river channel or on creeks to prevent flooding of surrounding land at high tides. These structures have the effect of truncating the reduced salinity zone and the tidal freshwater zone which can be important for some plant (e.g. reeds) and animal communities.

Abstraction of freshwater from rivers and groundwater supplies in river catchments can reduce the total amount and the temporal pattern of the freshwater flow into an estuary and influence the salinity regime. This is perhaps the most important factor affecting the salinity regime in estuaries, especially in England. The pattern of development in the river catchment, and in particular development on floodplains, can also influence the magnitude of flood events and so produce large episodic changes to the salinity regime in receiving estuaries.

Concentrations in estuaries range between 0.5 and 35 ppt, with the salinity at individual sites changing with the tidal ebb and flow. Concentrations in marine waters are much less variable, typically ranging between 33 and 35 ppt. Salinity may vary with depth in poorly mixed estuaries, since fresh river water flows over the denser saline water, forming a so-called salt wedge. In tidal rock pools, salinities can increase well beyond 35 ppt on hot, sunny days as freshwater evaporates.

Many estuaries have intensive monitoring programmes that include measurements of salinity. Relevant data will be available from the Environment Agency, SEPA or the Environment and Heritage Service.

The effects of changes to the salinity regime on the marine environment can be sub-divided into direct effects (those organisms directly affected by changes in the salinity regime) and secondary effects (those arising in the ecosystem as a result of the changes in the organisms directly affected).

The direct effects of changes to the salinity regime include:

• changes to water column structure (e.g. stratification) and water chemistry (e.g. DO saturation and turbidity);
• lethal and sub-lethal effects on marine organisms;
• behavioural changes in fish and macrocrustacean populations.

Changes to the freshwater flow can have temporal and spatial effects on water column structure in estuaries as a result of differing degrees of salinity induced stratification. The precise consequences will be estuary specific but could have implications for water quality and for the distribution of organisms in the water column and sediments.

Dissolved oxygen is more soluble in freshwater than saline water at constant temperature and, consequently, freshwater entering the estuary has the potential to have enhanced dissolved oxygen concentrations. Fluctuations in the salinity regime has the potential to influence dissolved oxygen concentrations. The distribution and transportation of suspended sediment and the deposition of fine grains in an estuary are driven by the mixing of seawater and freshwater. Any significant sustained changes to the freshwater flow have the potential to disrupt the cycles of deposition and erosion with the potential for adverse effects on certain habitats. For example, mudflats could have the supply of depositing material removed and begin to erode with a loss of associated benthic invertebrate communities and fish and bird feeding grounds.

All marine organisms have a range of tolerance to salinity which is related to their ability to regulate the osmotic balance of their individual cells and organs to maintain positive turgor pressure. Organisms are commonly classified in relation to their range of tolerance as:

• stenohaline (having a narrow range of tolerance) including most marine and freshwater organisms; and
• euryhaline (having a wide range of tolerance) including most truly estuarine species.

The reduction in the number of species with decreasing salinity in an estuary is a characteristic feature of these systems. For example, a typical marine rocky shore community may contain up to 100 macroalgal species, but at the freshwater end of an estuary, this may decrease to less than five macroalgal species. Benthic invertebrate communities also vary in response to salinity with diversity decreasing with decreasing salinity. Variations in salinity regime can modify community distribution and composition. This may be particularly evident at the head of an estuary where benthic invertebrate communities can vary between those typical of freshwater and those typical of an estuary, depending on the amount of freshwater flow entering the estuary during the summer.

Sub-lethal effects of changed salinity regimes (or salinity stress) can include modification of metabolic rate, change in activity patterns or alteration of growth rates (McLusky 1981).

Behavioural responses to changes in salinity regime can include avoidance by mobile animals, such as fish and macrocrustaceans, by moving away from adverse salinity and avoidance by sessile animals by reducing contact with the water by closing shells or by retreating deeper into sediments. The variations in salinity of interstitial waters within sediments are much less than in the water column. These responses are only successful for transient episodes of adverse salinity.

Salinity plays an important role in the cues for a number of migrations that take place within estuaries including those of crustaceans, such as shrimp and crabs, and of fish, such as salmon, flounder and smelt. Variations in freshwater flow within estuaries can determine the distribution of fish populations and potentially determine the success of a particular year class by affecting access to spawning or feeding grounds.

The principal indirect effect of changes in the salinity regime is a potential change in communities of secondary consumers (fish and birds) in response to changes in communities of benthic invertebrate and fish food organisms.

Potential effects include:

• changes to water column structure (e.g. stratification) and water chemistry (e.g. DO saturation and turbidity);
• lethal and sub-lethal effects on marine organisms resulting in changes in community distribution and composition;
• behavioural changes in fish and macrocrustacean populations with the potential to impact adversely on feeding and spawning migrations within and through estuaries;
• potential change in communities of secondary consumers (fish and birds) in response to changes in communities of benthic invertebrate and fish food organisms.

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