Little has been published about the interactions of metals and parasites in economically important aquaculture species, particularly shellfish. Metal bioaccumulation and parasitic diseases could vary in different species depending on temperature changes and other environmental factors. Most studies conducted on endoparasites, such as acanthocephalans, cestodes, nematodes, and trematodes, indicate that only cestodes and acanthocephalans could absorb heavy metals successfully in their hosts, and that only adult worms could be used as indicators of environmental pollution. In Artemia parthenogenetica, cestodes increased resistance to arsenic (As) pollution and temperature changes; and infection was associated with improved antioxidant defense system without oxidative damage. The most serious parasite of Penaeus spp. is Enterocytozoon hepatopenaei (Microsporidia: Enterocytozoonidae). Apostome ciliates are negatively impacting Pandalus borealis of the northeastern United States (Synophrya sp. that causes “white eggs” or Black Spot Gill Syndrome) and Penaeus spp. from the South Atlantic and Gulf of Mexico (Hyalophysa lynni that causes shrimp black gill). In freshwater fish, the larvae of the nematode Eustrongylides spp. Jägerskiöld, 1909 (Nematoda: Dioctophymidae) absorbed lead (Pb), mercury, and cadmium, when the metal levels were close to zero in water and sediment. The concentration of Pb in the larvae was approximately 17 times higher than in the fish. Like the antioxidant defense reactions in the parasitized A. parthenogenetica exposed to As, an improved antioxidant defense system may be available in parasitized fish, limiting oxidative damage caused by metals. This study presents baseline concentrations of 30 metals in wild Penaeus vannamei Boone, 1931 from Ecuador and other species, as well as the current taxonomy for selected shellfish species and their parasites. Research is needed to assess the relationship of metals in parasites and host tissues, and oxidative stress in shellfish. The tools of One Health including molecular ecology, population genomics, proteomics, and epigenetic epidemiology should be used to detect parasites and environmental pollution indicators that could threaten aquatic species from freshwater and marine ecosystems, particularly considering climate change and pollution threats.