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Eutrophication as one of the importunate environmental hazards in the aquatic ecosystems causes pronounced deterioration of the water quality and represents serious threat to the biotic components of this ecosystem. The main environmental effects of eutrophication are increase of suspended particles owing to extensive macroalgal blooms, decrease of water clarity, and increase in the rate of precipitation that led to the destruction of benthic habitat by shading of submerged vegetation. In addition, other important effects are also known such as the bottom-water hypoxia, production of CO2 associating the decomposition of intensive produced organic matter which enhances water acidification, and altering biogeochemical processes, including sediment anoxia, accumulation of deleterious hydrogen sulfide, and nutrient cycling. Shift in the phytoplankton community was frequently reported in numerous eutrophic coastal waters owing to the variable nutrient requirement of different phytoplankton groups and the ratios between the different nutrients in these waters. Eutrophication is often accompanied by algal blooms which are frequently harmful and cause various injuries to the aquatic animals, such as clogging of fish gills, poisoning by toxins secretion, and localized anoxia, which consequently lead to detrimental effect on the fishing resources and the national economy through mass mortality of variable aquatic animals. The hypoxia conditions in bottom waters cause escape of sensitive demersal and other benthic fishes, mortality of bivalves, echinoderms and crustaceans, and extreme loss of benthic diversity, which led to changes in the diet of bottom-feeding fishes as well as shift in dominance among demersal fish species. Increase of algal growth/organic production rates led to changes in the benthic community structure, such as replacement of hermatypic corals with coralline algae, filamentous algae, macroalgae, and/or a variety of filter feeders and increase of bioerosion in some forms. Trophic linkages between pelagic and benthic communities are affected by eutrophication in the coastal waters, where the feeding habit of higher consumers such as benthic fish changes to derive high percentage of their energy from pelagic primary production sources. Shellfishes as an intermediate link between the water column and demersal fish could also be affected by eutrophication and will impact (as prey) on the demersal fish production. Meanwhile, increasing turbidity with eutrophication led to a shift in fish species owing to change of feeding on zooplankton to benthic organisms. Severe shading and light attenuation caused by blooms of both macroalgae and phytoplankton in eutrophic conditions hinder the photosynthetic processes in benthic plants and has led to the decline of seagrass habitats. High nutrient levels may lead to disturbance in nitrogen and phosphorus metabolism in seagrass and consequently cause a change in plant communities. Coral reefs are affected by eutrophication in different aspects. The organic compounds released from algal blooms promote microbial activity on coral surfaces and cause coral mortality, while synergistic effect of both the dissolved organic matter and rates of bioerosion has a pronounced role in reef degradation. Harmful algal blooms caused a complete loss of the branching corals, and substantial reductions in the abundance, richness, and trophic diversity of the associated coral reef fish communities. Eutrophication and siltation have severely stressed many fringing and offshore reefs that prefer to grow in nutrient-poor waters, and cause physiological changes in growth and skeletal strength, decrease of reproductive effort, and a reduced ability to withstand disease. In many marine eutrophic habitats, zooplankton community experienced a decline in species richness and abundance, change in structure, size, reproduction rate, and feeding habits. Size change in zooplankton occurs owing to the replacement of small species by another relatively large species of the same group, while the structure may change because of the trophic relationship of zooplankton with their prey (primary producers) and predators (fishes). Although benthic foraminiferans have been widely used as indicators of eutrophication in coastal marine ecosystems, low species diversity and high population densities of several benthic foraminiferans were reported in eutrophic area. On the other hand, smaller opportunistic benthic foraminiferal species dominate in the coral reef ecosystems and lead to a decline of larger endosymbiont-bearing taxa, while the hypoxia-tolerant foraminiferan species increased in abundance against the disappearance of the more sensitive species.

The coastal area of Egypt on the Mediterranean Sea extends for about 1,200 km. It hosts a number of important residential and economic centres, like the cities of Alexandria, Port Said, Damietta, Rosetta, Matruh, and AL-Arish. The coastal strip between Alexandria and Matruh hosts tens of tourist villages, which are usually crowded by visitors during summer. Many activities are known in the coastal area, including fishing, industrial, tourism, trading and agricultural, oil and gas production, and transportation. There are five large ecologically different coastal lagoons connected to the sea coast, representing together about 25% of the total area of the Mediterranean wetland. These lagoons are considered as reservoirs for agricultural, industrial, and municipal wastes, which are discharged from surrounding cities and cultivated lands. The Egyptian Mediterranean coast receives huge volumes of wastewaters every year through the coastal lagoons and from other land-based effluents. These wastes are loaded by variable amounts and types of pollutants, in addition to great amount of nitrogenous and phosphorous compounds, which in turn cause high level of eutrophication along a significant part of the Mediterranean coast, particularly of both the Nile Delta region and Alexandria coast. Eutrophication is an importunate problem to the Egyptian Mediterranean coast, resulting in fundamental changes in the structure of the planktonic and benthic communities as well as fish mortality. Eutrophication was accompanied by the appearance of several harmful algal species at several hot spots along the coast. The level of eutrophication demonstrated wide variation along the Egyptian coast relative to the variations in the volume and contents of discharged wastes.