Fifteen water quality parameters and nine coral community variables were assessed in eight reef sites along the Red Sea coast of Egypt. Coral reef environments are suffering of stress from increased anthropogenic activities, particularly in the vicinity of heavily populated and touristic areas such as Hurghada, Ain Al-Sukhna and Sharm El-Sheikh. Increased terrestrial runoff of sediments, nutrients, organic matter and other pollutants are the main causes of water quality deterioration in the investigated reef sites. The results showed that bioerosion of corals by sea urchins, and enhanced abundance of macroalgae and consequent competitive overgrowth of corals were the major reasons of coral damage observed in the area of study. Population density of sea urchins exhibited significant and positive correlations with the majority of eutrophication parameters. Salinity was significantly and negatively correlated with live hard coral cover. Exceeding levels of DIN and TSM above the threshold concentrations for eutrophication were reported to be indirectly and adversely affecting coral reefs through stimulating the growth of macroalgae, enhancing sea urchin density and reducing water transparency. The results support the predictions of bottom-up hypothesis that confirm the critical role of eutrophication in structure of coral reef community.