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The single-beam acoustic ground discrimination system, Quester Tangent Corporation (QTC View, Series V), was applied to survey the Western (WH) and Eastern (EH) Alexandria harbors during 2011 to identify, map and compare the acoustic diversity of seabed. The surveys were conducted using echo sounder with frequency 50 KHz. The gradients were analyzed. The majority of the survey was carried out in shallow water, with the exception of the navigation channel in WH. The acoustic data obtained at one frequency was, individually, submitted to stacking, and clustering with a final solution of five acoustic classes in the WH and six acoustic classes in the EH. The acoustic survey was complemented with sampling and diver surveys. Throughout the grain size analysis and diver survey, the acoustic classes coincide with the result of grain size analysis. Study areas contain pollutant as indicated by the chemical analyses and diver observations. Bathymetric maps established by acoustic survey clarify that bottom slopes in study areas gradually increase towards the center of the harbors and El-Boughaz opening. The study includes the hydrographic data (Temperature, pH, etc ) and nutrient salts (ammonia, nitrite, nitrate, and phosphate). The nutrients were extensively supplied since a long time ago from the main station at Kayet Bay as well as subsidiary 11 outfalls. It receives an amount of about 80,000 m 3 /day of untreated sewage which affects the physical, and chemical characteristics of the EH water quality. High values of ammonia (3.6 μM), Nitrate (1.4 μM) and Nitrite (1.6 μM) were recorded for surface water in the EH. Phosphate showed narrow range of variation between surface and bottom water of EH and WH. The analyses in the WH give the maximum values for Ammonia 4.0 μM, Nitrate 1.6 μM, Nitrite 0.19 μM and Phosphate values ranged between 0.3 and 0.5 μM. The benefits of this research is to identify the presence of sunken antiquities in the EH which have been confirmed by divers photographs, having detailed bathymetric maps, and identify the sea bed characteristics for Alexandria harbors. It is necessary to follow- up the biological and chemical changes in surface and bottom waters to trace sources of pollution and take necessary actions to protect water resources. [ABSTRACT FROM AUTHOR]