The main culprits towards the transmission of infectious disease are the filter feeders - notably sea urchins and shellfish. These can become contaminated during handling, but they can also bear pathological organisms acquired from their marine environment. Filter feeders gathered near a sewage outlet will contain numbers of sewage bacteria, including both pathogenic enterobacteria and viruses. Outbreaks of typhoid fever have frequently arisen from the consumption of contaminated shellfish, and outbreaks of infectious hepatitis have been traced to oysters contaminated with the viral agent of this disease.

Fish can also become contaminated superficially with a variety of bacterial forms including many marine halophilic and psychrophilic bacteria. The "phosphorescence" of spoiling fish is due to the growth of luminescent marine bacteria (such as Achromobacter) on the surface. Uncooked fish (e.g. mullet) can result in intestinal fish fluke of humans: Heterophyes heterophyes and Metagonimus yokogawai.

Since most Mollusca species are filter-feeders, the edible species can bear pathological organisms acquired from their marine environment thus contributing to outbreaks of typhoid and infective hepatitis. They can also have high heavy metal levels. The level of lead in sea sediments in the vicinity of the capital city was found at 118 ug/g to be markedly higher to levels of other Mediterranean inshore sediment exposed to urban and industrial pollution [Thermaikos Gulf: 71 ug/g; Gulf of Venice: 45 ug/g]. Certain edible filter-feeder shellfish, such as the Date Mussel [Lithophaga lithophaga] and the Warty Venus [Venus verrucosa], collected from Maltese waters have also been found to carry high lead levels. The main source of this high sediment lead is most likely to be car traffic rain wash-off.