Marine calcifying organisms on coral reefs are under threat from a range of anthropogenic stressors. Understanding their biomineralization pathways in different reef environments is key to unravelling their response to a rapidly changing ocean. Turbid reefs are forecast to increase throughout the 21st century and are resilient conservation hotspots, yet understudied due to a lack of information resolving biomineralization processes. Herein, for the first time, we assess the crystallographic and geochemical signatures of aragonite giant clam shells Tridacna squamosa from high and low turbid reefs in the Coral Triangle. Shell composition is strongly influenced by turbidity and biominerals formed in a high turbid reef show a more organized crystal orientation and significantly lower element-to-calcium ratios (Magnesium/Calcium, Strontium/Calcium). We hypothesize that these variations are driven by physiological changes related to the trophic flexibility of T. squamosa. Observed differences have implications for biomechanical and defence responses of shells, important in their ability to survive future change.