A fifteen-month fortnightly survey of microbial health risk indicators and pathogens has been carried out at 25 freshwater recreational and water supply sites distributed throughout New Zealand, for: E. coli, Clostridium perfringens spores, F-RNA bacteriophage, somatic coliphage, human enteroviruses, human adenoviruses, Cryptosporidium oocysts, Giardia cysts, Salmonella and Campylobacter. Sites were selected to represent five geographical areas covering New Zealand and five categories of predominant environmental impact: birds, dairy farming, forestry/undeveloped, municipal, and sheep/pastoral farming. Six of the sites were also source waters for treated drinking-water supplies. Of the indicators, E. coli was detected in 99 % of all samples, with somatic coliphage being detected most of the time (89 %). Of the pathogens tested, Campylobacter and human adenoviruses were inferred to be the most likely to cause human waterborne illness to recreational freshwater users. Using data from all sites, an estimated 5 % of notified campylobacteriosis cases in New Zealand could be attributable to water contact recreation. The critical value for E.coli as an indicator of increased Campylobacter infection is in the range of 200–500 E. coli per 100 ml. This result has been used to derive new national water quality guidelines for recreational fresh water in New Zealand.