The protozoan parasites Giardia and Cryptosporidium have been described as important waterborne disease pathogens, and are associated with severe gastrointestinal illnesses. The objective of this paper was to investigate the presence of Giardia cysts and Cryptosporidium oocysts in samples from watershed catchments and treated water sources. A total of 25 water samples were collected and examined according to the US EPA—Method 1623, 2005, consisting of 12 from drinking water and 13 from raw water. Positive samples from raw water for Giardia cysts and Cryptosporidium oocysts were 46.1 and 7.6%, respectively. In finished water, positive samples were 41.7% for Giardia cysts and 25.0% for Cryptosporidium oocysts. Concentrations of Giardia cysts found in raw water samples ranged from “not detected” to 3.4 cysts/L, whereas concentrations of Cryptoporidium oocysts ranged from “not detected” to 0.1 oocysts/L. In finished water, Giardia concentrations ranged from “not detected” to 0.06 cysts/L, and Cryptosporidium, from “not detected” to 0.01 oocysts/L. Concentrations of Giardia cysts and Cryptosporidium oocysts were not high in the samples analyzed. Nevertheless, the results of this study highlight the need to monitor these organisms in both raw and drinking water.