The accurate characterization of coral reef habitats not only supplies invaluable data to marine researchers but also provides conservation managers the necessary information to protect these fragile ecosystems. Without accurate in situ documentation of benthic coral reef communities, the general health, as well as the effects of stressors on these habitats, cannot be correctly quantified for scientific evaluation. In this study, the benthic ecological assessment for marginal reefs (BEAMR), a comprehensive monitoring protocol for reef characterization, was applied to a nearshore coral reef system in the southeast region of the Gulf of Mexico to determine if the condition of the habitat had negatively altered over the study's duration. BEAMR data sets were collected in three separate sampling events over 5 years, with sampling scheduled around an experimental application of beach compatible sand adjacent to the study area. The results from PRIMER-E v.6 statistical analyses showed that the marine reef community as a whole (i.e., integration of all benthic functional groups) was not negatively affected throughout the study's duration. Additionally, parametric statistical analyses showed that the coral reef habitat in this Gulf region did not sustain significant influxes of sediment or adverse effects to the biota, but rather showed a significant increase in stony coral colony size and cover over time. Overall, it was determined that the condition of this reef resource has maintained a positive level of sustainability during this study, and by using the BEAMR method, marine biologists were able to statistically quantify the health of a coral reef system. Even so, the vulnerability of reef resources remain, which is why specific habitat assessment protocols, such as the BEAMR method, help support the worldwide conservation of coral reef communities. By aiding in the quantification of reef health, BEAMR can help identify and characterize potential reef effects from both natural and human pressures.