Livestock, humans and wildlife are generally believed to be major contributors of Cryptosporidium contamination in surface waters in Canada. Cryptosporidium is a relatively strict host-specific parasite, and molecular typing of Cryptosporidium is emerging as an effective fecal source tracking tool. The Cryptosporidium species/genotypes commonly identified in water can yield insights into the nature of anthropogenic inputs (i.e., human or animal waste) and thus help inform source water protection strategies. Detection of Cryptosporidium forms harboured by the dominant livestock species within a watershed should be evidence for agricultural contamination. To challenge this hypothesis, parasite occurrence and molecular profiling were used to track fecal contamination in watersheds heavily dominated by swine production (the Bras d,Henri/Fourchette watershed, QC), beef or dairy cattle (Oldman watershed, AB; South Nation watershed, ON), and intensive poultry farming (the Sumas watershed, BC). Parasites were monitor on a bi-weekly basis from the spring to the fall of 2006 using USEPA Method 1623. Levels of Cryptosporidium contamination ranged widely through the sampling period with average watershed values peaking at 0.77 oocysts/litre for the Bras d,Henri/Fourchette watershed; 0.86 oocysts/litre for the South Nation watershed; 0.36 oocysts/litre for the Oldman watershed; and 0.21 oocysts/litre for the Sumas watershed. Molecular forensic profiling of Cryptosporidium positive microscope slides at high occurrence levels from these watersheds resulted in 4 species/genotypes from the Bras d,Henri/Fourchette watersheds (C. andersoni, muskrat II genotype, W7 genotype and W15 genotype); 6 from the Oldman (C. andersoni, C. baileyi, cervine genotype, muskrat II genotype, skunk genotype and W15 genotype); 6 from the South Nation (C. andersoni, C. parvum, muskrat II genotype, muskrat I genotype, W7 genotype and W12 genotype) and 4 species/genotypes from Sumas watershed (C. muris, opossum I genotype, muskrat I genotype, W15 genotyp). Wildlife species of Cryptosporidium were commonly found in all four watersheds. Surprisingly, only in the cattle-dominated watersheds (Oldman and South Nation) did Cryptosporidium species occurrence correlate with the dominant livestock species farmed (i.e., a predominance of C. andersoni). In poultry and swine dominated watersheds (Sumas and Bras d,Henri/Fourchette watersheds, respectively) the diversity of Cryptosporidium observed in the water did not appear to correlate with host-adapted forms associated with the dominant animal agriculture activity (i.e., C. meleagridis, C. baileyi, C. suis or pig genotype II). These preliminary findings did not support the stated hypothesis indicating that genotyping tools are necessary for determining the animal hosts responsible for contributing parasites into the watershed. © 2007 American Water Works Association.