The Gulf of Aqaba is home to three giant clam species with differing ecological niches and levels of photosymbiotic activity. Giant clams grow a two-layered shell where the outer layer is precipitated in close association with photosymbiont-bearing siphonal mantle, and the inner layer is grown in association with the light-starved inner mantle. We collected 38 shells of the three species (the cosmopolitan Tridacna maxima and T. squamosa, as well as the rare endemic T. squamosina), and measured carbon and oxygen isotope ratios from inner and outer shell layers, to test for differences among species and between the layers of their shells. T. squamosina records higher temperatures of shell formation as determined by oxygen isotope paleothermometry, consistent with its status as an obligately shallow-dwelling species. However, the known negative fractionation imparted on tissue carbon isotopes by photosymbiotic algae did not produce measurable offsets in the carbonate δ13C values of the more symbiotic T. squamosina and T. maxima compared to the more heterotrophic T. squamosa. Across all species, outer shell layers recorded mean growth temperatures 1.8 °C higher than corresponding inner layers, which we propose is a function of the high insolation, low albedo microenvironment of the outer mantle, and potentially the activity of the symbionts themselves. Population-wide isotopic sampling of reef-dwelling bivalve shells can help constrain the ecological niches of rare taxa and help reconstruct their internal physiology.