Shellfish are filter feeders, and may concentrate microorganisms (bacteria and viruses), as well as natural toxins and chemicals if they are present in the growing waters. The current National Shellfish Sanitation Program (NSSP) dictates uniform requirements that every state must meet, with federal oversight provided by the U.S. Food and Drug Administration (FDA). States are required by the NSSP to maintain minimum sanitation standards addressing issues such as water quality monitoring, harvest area enforcement, training of harvesters and dealers, processing, shipping, and handling.

Flinders University researchers measured microplastics levels in South Australian mussels, and the findings indicate the probability of plastic pollution in the global food supply chain.