Cryptosporidium and Giardia (oo)cyst concentrations are frequently used for assessing drinking water safety. The widely used USEPA Method 1623 provides total counts of (oo)cysts, but may not be accurate for human health risk characterization, since it does not provide infectivity information. The total counts and infectious fraction of Cryptosporidium oocysts and the total counts of Giardia cysts were assessed in major fecal pollution sources. Fresh calf and cow feces, their manure, and the discharge point were sampled in a small rural sub-watershed (n = 20, 21, 10, 10). Median concentrations for total (oo)cysts were higher in calves (333 oocysts g−1; 111 cysts g−1) than in cows (52 oocysts g−1; 7 cysts g−1). Infectious oocysts were found in 17 (7%) of the samples and none were found in manure or at the discharge point. Urban sources were sampled in the influent and effluent (n = 19, 18) of two wastewater treatment plants. Peak concentrations were 533 oocysts L−1 and 9,010 cysts L−1 for influents and 89 oocysts L−1 and 472 cysts L−1 for effluents. Infectious oocyst fractions varied from below the detection limit to 7–22% in the effluent and influent respectively. These infectious fractions are significantly lower than those currently used for quantitative microbial risk assessment estimates.