Due to the scarcity of the proper access point to the deep waters by divers and snorkelers, bays and lagoons are used as sheltered marine areas in the southern Egyptian Red Sea and are represented very valuable recreational areas. With the recent booming in tourism along the Egyptian coast of the Red Sea, the sheltered bays and lagoon reefs are tremendously impacted by recreational SCUBA diving activities. Three bays with similar environmental and topographic characteristics, but with different levels of diving and snorkeling activities were selected to study the impacts of recreational SCUBA diving on sedimentation rate, substrate analysis, coral cover, diversity, coral recruitment and coral reef fish assemblages. In addition to the expected physical damage causes by incidental contacts to corals by divers, the results showed that increasing sedimentation rate as a result of intensive SCUBA diving also caused a serious impact on coral reef communities of the surveyed bays. Highest sedimentation rate was estimated at the over-dived site of the Marsa Um El-Gurifat (approximately 51,000 divers per year). Walking and standing of divers on the sea floor was disturbing the fine sediments of the bay floor, increasing turbidity and sedimentation rate on the nearby coral reefs of the bay. High sedimentation rate on the reefs of Marsa Um El-Gurifat caused the following: reduced the coral cover; overgrown soft coral that dominated coral cover, reduced the recruitment of new coral colonies, increased dead coral cover, increased the macroalgal cover especially on the reef flat areas, decreased the diversity of hard coral and coral reef fishes, shifted the fish assemblage toward higher occurrence of herbivore fishes comparing with corallivore and carnivore ones.