Despite increased recognition of the risks to the health of humans and the environment, untreated municipal wastewaters are still discharged into waterways worldwide. One of the primary concerns related to its discharge into surface waters is the risk to human health through the transmission of pathogens associated with faecal matter. Saint John, New Brunswick, is one of the few Canadian cities that still releases untreated sewage into its urban waterways and harbour. Water faecal coliform levels, an indicator of faecal waste and associated pathogens, are well above recreational guidelines in some of these areas. Although it is not encouraged by the municipality, recreational fishing occurs in these areas and this raises concerns regarding the potential for disease transmission during the handling of these fish. To investigate the potential for fish to be a vehicle of pathogen transmission to humans, the skin of wild fishes (smelt, Osmerus mordax, and mummichog, Fundulus heteroclitus) and caged mummichog was sampled for faecal coliforms from several sites in Saint John between August and November of 2005. Water faecal coliform levels at sites used for caging studies and wild fish collections, and the duration of caging were compared with the number of faecal coliforms on the surface of the fish. Skin samples from the two fish species collected from the wild indicated elevated levels of fecal coliforms in some locations. Both wild and caged fish showed that the amount of faecal coliform on fish skin is influenced by the water faecal coliform levels.