Aquaculture, which is growing 3-5 times faster than terrestrial agriculture, will play an important role to meet future global food production needs. However, over 80% of global sewage production is returned to the environment untreated or poorly treated. In developing nations, these nontraditional waters of diverse quality are being recycled for aquaculture, yet chemical residues are differentially studied. Here, we examined pharmaceuticals, pesticides, polychlorinated biphenyls (PCBs), polybrominated diphenyl ethers (PBDEs), polycyclic aromatic hydrocarbons (PAHs), and flame retardants in marine bivalves using isotope dilution liquid chromatography-tandem mass spectrometry (LC-MS/MS) and low-pressure gas chromatography-tandem mass spectrometry (LP GC-MS/MS). Green-lipped mussels from the field and oysters from aquaculture net pens, which are harvested as food products, were collected adjacent to point source municipal wastewater and landfill leachate effluent discharges, respectively, in Hong Kong, the fourth most densely populated country in the world. Multiple classes of pharmaceutical, pesticides, PAHs, and phosphorus-based flame retardants were detected at low μg/kg levels. Acceptable servings per week indicated minimal risk for a number of chemicals; however, such calculations could not be performed for other contaminants of emerging concern. Future efforts are needed to better understand contaminant influences on marine bivalve populations and aquaculture product safety, particularly in rapidly urbanizing regions of developing countries with limited wastewater infrastructure.