A four-year systematic study of microbial water quality in the surface waters of central Arizona was performed. The objectives of this study were to investigate the occurrence of microbial pathogens and indicators in the waters. A total of 192 water samples from five sites were analyzed for Cryptosporidium, Giardia, and various microbial and physical indicators. Ten percent (16/162) of the samples collected using EnviroChek filters were positive for Cryptosporidium oocysts, whereas no oocysts (<1 in 5 L) were detected in the grab samples (0/30). Giardia cysts were detected in 10% (3/30) of the grab samples and in 27% (44/162) samples collected using EnviroChek filters. Mean concentrations of oocysts in the source waters at the treatment plants were lower than the Bin 1 category of the USEPA Long Term 2 Enhanced Surface Water Treatment Rule; therefore no additional treatment is required by the plants. The annual risks of infection from Cryptosporidium met the annual acceptable risk of 10−4 at all sampling sites, whereas the risks of Giardia infection at the Verde River and the Salt River were 5.70E-04 and 2.66E-04, respectively.