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Eutrophication problem in El Gouna shallow artificial coastal lagoons in Egypt was investigated using 2D TELEMAC-EUTRO-WAQTEL module. Eight reactive components were presented, among them dissolved oxygen (DO), phosphorus, nitrogen, and phytoplankton biomass (PHY). The effect of warmer surface water on the eutrophication problem was investigated. Also, the spatial and temporal variability of the eutrophication was analyzed considering different weather conditions: tide wave, different wind speeds and directions. Moreover, effect of pollution from a nearby desalination plant was discussed considering different pollution degrees of brine discharge, different discharge quantities and different weather conditions. Finally, new precautions for better water quality were discussed. The results show that tide wave created fluctuations in DO concentrations, while other water quality components were not highly influenced by tide’s fluctuations. Also, it was found that high water temperatures and low wind speeds highly decreased water quality producing low DO concentrations and high nutrients rates. High water quality was produced beside inflow boundaries when compared to outflow boundaries in case of mean wind. Moreover, the results show that the average water quality was not highly deteriorated by the nearby desalination operation, while the area just beside the desalination inflow showed relatively strong effects. Different weather conditions controlled the brine’s propagation inside the lagoons. Moreover, increasing the width of the inflow boundaries and injecting tracer during tide and mean wind condition are new precautions which may help to preserve the water quality in a future warmer world. This study is one of the first simulations for eutrophication in manmade lagoons.