Zebra mussels (Dreissena polymorpha) from throughout the Shannon River drainage area in Ireland were tested for the anthropozoonotic waterborne parasites Cryptosporidium parvum, Giardia lamblia, Encephalitozoon intestinalis, E. hellem, and Enterocytozoon bieneusi, by the multiplexed combined direct immunofluorescent antibody and fluorescent in situ hybridization method, and PCR. Parasite transmission stages were found at 75% of sites, with the highest mean concentration of 16, nine, and eight C. parvum oocysts, G. lamblia cysts, and Encephalitozoon intestinalis spores/mussel, respectively. On average eight Enterocytozoon bieneusi spores/mussel were recovered at any selected site. Approximately 80% of all parasites were viable and thus capable of initiating human infection. The Shannon River is polluted with serious emerging human waterborne pathogens including C. parvum, against which no therapy exists. Zebra mussels can recover and concentrate environmentally derived pathogens and can be used for the sanitary assessment of water quality.