The occurrence of waterborne pathogens was investigated at three drinking water intakes located about 2 km offshore in Lake Ontario. Water sampling was conducted over 3 years for
Campylobacterspp., Cryptosporidiumspp., Giardiaspp., cultivable enteric viruses, and water quality parameters. All pathogens were detected in the offshore source water for each water treatment plant (WTP1 to WTP3), although at relatively low frequencies and concentrations. Giardiawas the most common pathogen, occurring in 36% of water samples from the influent of WTP1 ( n= 46), and with a maximum concentration of 0.70 cysts/liter in this influent. Cryptosporidiumoccurred as frequently as 15% in the WTP2 influent ( n= 35), with a maximum concentration of 0.40 oocysts/liter in the WTP1 influent. The human BacteroidalesHF183 DNA marker was most common in the WTP1 influent (19%), and this was the only WTP where the Cryptosporidium hominisgenotype was detected. No water quality parameter was predictive of pathogen occurrence across all three WTP influents. Escherichia coliwas often below detection when pathogens were detected, and spikes in E. coliconcentrations often did not coincide with pathogen occurrence. After summer rain events, river plumes had E. coliconcentrations as high as 222 CFU/100 ml in surface waters 2 km offshore, without impacting drinking water intakes below the thermocline on the lake bottom. At times, prechlorination to control mussels at offshore intake cribs compromised the use of E. colifor “raw” water quality assessment, particularly for chlorine-resistant Cryptosporidium. E. colimeasured by standard methods did not reliably predict pathogen occurrence at drinking water intakes in offshore ecosystems.