Sentinel freshwater mussels(Hydridella menziesi)were immersed in rivers at sites impacted by faecal pollution. The indicator bacterium,Escherichia coli, was recovered from all mussels including those at a forest control site, but concentrations were highest at sites impacted by either treated sewage or treated meat‐processing waste water, or by inputs from dairy farms. The three pathogens sought were recovered from mussels, except those at the forest (control) site:Campylobacter jejuniandCampylobacter coliat treated sewage sites;Salmonella typhimuriumandC. jejuniat treated meat‐processing waste water sites; andC. jejuniandYersinia enterocoliticaat sites impacted only by dairy farms. The FRNA bacteriophage concentration was high in mussels impacted by sewage or sheep‐processing waste water but was low when the input was only from dairy farms. Mussels up to 23 km from a sewage discharge contained a high concentration of FRNA suggesting that there could be a health risk due to viruses, although the water did not exceed recommended guidelines. Pathogens were also sought in untreated waste waters.C. jejuniandC. coliwere recovered from both sheep‐processing and beef‐processing waste waters and the only sewage isolate identified was confirmed asC. coli. Salmonellaspp. were recovered from all waste waters, withS. typhimuriumphage type 135, isolated from a sample of meat‐processing waste water, and from mussels immersed 1 and 5 km down stream of that plant's discharge.Y. enterocoliticawas recovered from most samples of animal waste water. It appears that pathogens are introduced into New Zealand rivers by all major sources of faecal contamination.