Surface inland and coastal waters in Ireland were surveyed for the human waterborne enteropathogens; Cryptosporidium parvum, Giardia lamblia, Encephalitozoon intestinalis, Encephalitozoon hellem, and Enterocytozoon bieneusi by utilizing bivalve mussel species, i.e., Mytilus edulis (blue mussel), Anodonta anatina (duck 'mussel', actually a unionid clam), and the invasive Dreissena polymorpha (zebra mussel) as biomonitors at twelve sites located in three Irish river-basin districts with various water-quality pressures. Biomolecular techniques were utilized to assess the presence and concentration of these pathogens. At least one pathogen species was detected in shellfish at each site. Cryptosporidium, implicated in several recent Irish gastrointestinal epidemics, was recorded at all sites subjected to agricultural runoff and at one sewage discharge site, linking source-track directly to human and animal fecal wastes. G. lamblia was present at eleven of the twelve sites in a range of concentrations. A coastal bay with raw urban sewage discharge was 100% positive for all analyzed enteropathogens. Overall, the results demonstrate long-term human enteropathogen contamination of Irish waters with consequent public-health risk factors for drinking-water abstraction and water-based activities.