The water in the canals and some recreational lakes in Amsterdam is microbiologically contaminated through the discharge of raw sewage from houseboats, sewage effluent, and dog and bird feces. Exposure to these waters may have negative health effects. During two successive 1-year study periods, the water quality in two canals (2003 to 2004) and five recreational lakes (2004 to 2005) in Amsterdam was tested with regard to the presence of fecal indicators and waterborne pathogens. According to Bathing Water Directive 2006/7/EC, based on Escherichia coli and intestinal enterococcus counts, water quality in the canals was poor but was classified as excellent in the recreational lakes. Campylobacter, Salmonella, Cryptosporidium, and Giardia were detected in the canals, as was rotavirus, norovirus, and enterovirus RNA. Low numbers of Cryptosporidium oocysts and Giardia cysts were detected in the recreational lakes, despite compliance with European bathing water legislation. The estimated risk of infection with Cryptosporidium and Giardia per exposure event ranged from 0.0002 to 0.007% and 0.04 to 0.2%, respectively, for occupational divers professionally exposed to canal water. The estimated risk of infection at exposure to incidental peak concentrations of Cryptosporidium and Giardia may be up to 0.01% and 1%, respectively, for people who accidentally swallow larger volumes of the canal water than the divers. Low levels of viable waterborne pathogens, such as Cryptosporidium and Giardia, pose a possible health risk from occupational, accidental, and recreational exposure to surface waters in Amsterdam.