In this study, we studied the environment factors such as plastics and heavy metals affecting the blood and cloacal microbiome of green (Chelonia mydas) and hawksbill (Eretmochelys imbricata) in captivity. By non-metric multidimensional scaling analysis, data has shown that the environment factors (p = 0.02), rather than species differences (p = 0.06), significantly influenced the composition of the cloacal microbiota of green and hawksbill turtles. The cloacal microbiota of both captive green and hawksbill turtles was dominated by several similar dominant phyla at differential abundance. Green turtles' cloacal microbiome was made up of 46% of Proteobacteria, 31% of Bacteroidota, 11% of Campylobacterota and 4% of Firmicutes, while the hawksbill turtles' cloacal microbiome was made up of 33% of Bacteroidota, 18% of Firmicutes, 17% of Proteobacteria, and 2% of Campylobacterota. Water conductivity, salinity, microplastic polymers (polycarbonate, polyethylene terephthalate, polystyrene), and copper are positively associated (p <
0.05) with blood urea nitrogen. Hematocrit and hemoglobin were found also negatively correlated (p <
0.05) with water pH, polyethylene terephthalate, iron, lead and zinc. The correlations established in this study shed light on the intricate interplay between water quality and the physiological responses of sea turtles. Recognizing these relationships is pivotal for monitoring and preserving the well-being of sea turtles in their natural habitats.