Environmental contamination of marine habitats is a global concern, especially in areas that are crucial for endangered species’ life cycles. To gain a comprehensive understanding of environmental contamination, analyzing various biotic and abiotic components of ecosystems is necessary. Situated in the Arabian Peninsula, Ras al-Jinz Reserve serves as an invaluable nesting site for green sea turtles (Chelonia mydas). There, the prevalence of antibiotic-resistant microbial strains and heavy metals was assessed by collecting samples from diverse components of this ecosystem, including sand from turtle nests, dead turtle hatchlings, fresh turtle eggs, oviductal fluids from nestling turtles, turtle carapace smears, live crabs, and seawater. Microbial fauna was identified using a MALDI-TOF Biotyper. The concentration of heavy metals was measured by an inductively-coupled plasma mass spectrometry. Among the isolated bacterial strains, 70 heterotrophic species belonging to eleven genera were identified, with over 46% of isolates belonging to the Pseudomonas species. More than 85% of isolates displayed antibiotic resistance but had negligible resistance to chloride. Of the 23 heavy metals assessed, Titanium and, in lesser measure Vanadium, were found in the highest concentrations, reaching up to 12 µg g-1. While such concentrations might not be immediately alarming, they are significant enough to warrant attention due to the potential health and environmental impacts. These results obtained over a decade after the last monitoring in the Reserve provide compelling evidence of the persistent presence of antibiotic-resistant bacteria. Additionally, the study confirms the prevalence of heavy metals, the sources of which remain unknown but are likely from anthropogenic sources. It is crucial to implement measures that mitigate sea turtles’ exposure to contaminants in Ras al-Jinz Reserve. Regular monitoring efforts are required to assess the emergence of discernible contamination trends in this critically important area.