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According to Little (2000), an estuary is a partially confined coastal mass of water with one or several streams or rivers flowing into it, and having connection to the open sea. Estuaries act as a transition region between ocean environments and river environments and are focus to both oceanic influences, for instance waves, the influx of saline water, and tides; and riverine influences, for example the flows of sediment and fresh water. The inflow of both freshwater and seawater bring about increased levels of nutrients in both sediment and the water column, forming estuaries among the leading productive natural habitats globally. Estuarine health can be defined as the diversity and copiousness of the benthos in the estuarine ecosystem.

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A health estuary can maintain and support a variety of different animals and plants and in due case the biodiversity of the estuary is maintained. Healthy estuaries operate in productive and special manner as they recycle and store nutrients, entrap sediments and create a buffer between the marine environment and coastal catchments, and they soak up, trap and remove toxins from pollutants, playing the role of natural water filters. This is very significant hat the processes can take place for an estuary to stay healthy. Estuaries support a variety of different habitats for instance salt marshes, mangroves, mudflats and sea grasses among others (Schwartz, 2005).

The health issues facing Australian estuaries are classified into chemical, physical, and biological. The sedimentation processes and the hydrological process comprise of the physical health issues. Estuaries receive sediments from the inflowing rivers, material generated within the estuary itself, and from the sea. High turbidity can be associated with increased sedimentation in most estuaries, and this can result into inhibition of light penetration hence limiting primary productivity thereby limiting on nutrient cycling. Sediments are rich in organic derived matter hence supplying a lot of nutrients which can result into eutrophication. The increased populations of aquatic plants which can result from the adequate nutrients bring about oxygen deficiency in the water thereby affecting aquatic life negatively.   In the case of hydrology, absence of flushing results into anoxia and high concentration of sulphide and ammonia thereby limiting spawning. Water can as well wash the harmful chemicals from dry land into the estuary and the chemicals can intoxicate the aquatic life (Gordon, 2004).   

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Increased populations of both plants and animals in aquatic life, and habitat destruction comprise of the biological health issues. Very many aquatic animals per unit volume of water can lead to depletion of aquatic plants thereby reducing the amount of oxygen for aquatic life due to a condition referred to as anoxia. This is because plants release oxygen and absorb carbon dioxide during the process of photosynthesis. It is also true that increased population of aquatic plants can also bring about anoxia as well bar the free movement of aquatic animals like fish. Land clearing has decreased the diversity and extent of terrestrial vegetation in Victoria since European settlement. This has decreased the habitat diversity of Victoria's estuarine catchments. Land use changes like land clearing can impact on the quality and quantity of freshwater flow by disturbing overflow rates, and the input rates of woody debris, chemical pollutants, and sediments (Little, 2000).

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Changes in salinity and the dissolved organic carbon comprise of the chemical health issues that affect life in estuaries. Salinity can change in a daily basis due to tides, and can change seasonally due to runoff. The aquatic plants and animal that survive in waters with low amount of dissolved salts can die incase the concentration of salts increase. The increased concentration of dissolved organic carbon colors the water brown hence affecting the penetration of light into water, and lowers the pH of water. Aquatic plants suffer due to inadequate light as the process of photosynthesis is hindered. Most aquatic life does not do well in acidic conditions which are as a result of lowered pH of water (Clarke, 2000).    

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According to Little (2000), ecological indicators are the strategies used to put across information concerning ecosystems and the consequences of man's activities on ecosystems to the public or to those involved in making government policy. Since ecosystems are complex ecological indicators help describe them in less complicated terms that can be comprehended and used by laymen to make decisions regarding management. The estuarine indicators used in Australia are temperature of water, salinity of water, water turbidity, dissolved oxygen and pH of water.

Temperature of water as an indicator can be used everywhere and is very cheaper since a mere thermometer can be used. The problem with using temperature as an indicator is that living thing are made up of proteins which can be denatured due to high temperature and hence no meaningful results. Salinity is very effective but expensive due to the use of expensive field meter. Turbidity is a very crucial indicator of a Coastal, Estuarine and Marine (CEM) condition.  Use of pH as an indicator is very effective and cheaper since it uses less expensive materials like universal indicator and pH meter. Using dissolved oxygen as an indicator is as well effective but it is involving since the dissolved oxygen can vary significantly over 24 hours (Day, 1989).

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