This study examined water and sediment samples for a range of indicator and pathogenic microorganisms from six sites in an urban estuary, Sydney, Australia. Water quality was affected by rainfall and sewage overflows which were associated with significant increases in the concentration of faecal coliforms, faecal streptococci, Clostridium perfringens spores, F-RNA bacteriophage, Aeromonas spp., Giardia and Cryptosporidium spp. However, in sediments, only faecal coliform concentrations were significantly increased by rainfall, although sewage overflow again resulted in increased concentrations of faecal coliforms, faecal streptococci, C. perfringens spores and Aeromonas. Isolation of Salmonella appeared to coincide with wet weather events and occasionally identical serotypes were detected in sediments at several locations within the estuary. However, isolations of enteric virus were sporadic and did not appear to be exclusively related to wet weather events. C. perfringens was identified as the most useful indicator of faecal pollution and was the only indicator significantly correlated to the presence of pathogenic Giardia (r = 0.41, p < 0.05) and the opportunistic bacterial genus Aeromonas (r = 0.39, p < 0.05). F-RNA bacteriophage was not significantly correlated with any of the pathogens examined.