Because of the pivotal role of the substrate composition in the ecological state of coral reef communities, the present study was attempted to investigate the substrate cover, coral reefs, and reef fishes in the marine ecosystem of the Wadi El-Gemal National Park (WGNP), Red Sea, Egypt. The surveys were conducted in the Spring and Autumn of 2015 by SCUBA diving and/or snorkeling. We applied the Point, Line, and Belt Intercept Transect (PIT, LIT and BLT) methods, to assess the state and forms of the substrate, through a quantitative assessment of the fundamental components of the benthic cover. A quantitative assessment was conducted on five main benthic categories at WGNP; hard corals, soft corals, dead corals, sand, and rocks. Six invertebrate groups; banded coral shrimp, sea urchin, sea cucumber, the crown of thorn, giant clam, and Drupella sp. were also investigated. The study showed that, while there was no significant difference between sites in the benthic structure and cover, sites were different in the cover of hard coral, the abundance of benthic invertebrates, and the abundance of reef fishes. We also, assessed the status of eight impact indicators of reef damage (or damage indication categories); old dead, recently dead, total bleached, partial bleached, diseased, broken, fragments, and recruitments of corals at the marine protected area as well as investigated the coral reef/reef fish community relationship. Among the eight reef impact indicators that were assessed in the current study, the old dead corals showed the highest cover of the substrate. In the same context, the cover of the diseased colonies was lower than other categories in the area of the study. The study also indicated that increasing hard coral cover in the study area had strongly affected the abundance of reef fishes. Nevertheless, the abundance of reef fishes was found to be increased with the increase of the hard coral cover (P < 0.05, r = 0.8), and this trend was attained by all reef fish families, the highest sites in coral cover and fish abundance were: Hnakourab, Wadi Lahmy and Sharm El-Luli (32, 28 and 25%, and 9, 11 and 6 mean number of fish/20 m transect), respectively. Positive correlation between the hard coral cover and fish abundance was detected as well. Acanthuraidae displayed the highest mean number of individuals (53.25/20 m belt transect). The study concluded that there is a need to perform a periodic assessment of the benthic cover of the main components of coral reef communities. Also, the study emphasized the role of benthic substrate structure and cover in the reef fish ecology.