A quantitative microbial risk assessment (QMRA) of Cryptosporidium, Giardia and diarrhegenic Escherichia coli (DEC) infection was performed using Monte Carlo simulations to estimate the human health risks associated with the use of canal water for recreational purposes, unrestricted and restricted irrigation in a tropical peri-urban area. Three canals receiving municipal, agricultural, and, predominantly, industrial wastewater were investigated. Identification of pathogenic protozoans revealed the major presence of Cryptosporidium hominis and both assemblages A and B of Giardia lamblia. The highest individual infection risk estimate was found to be for Giardia in an exposure scenario involving the accidental ingestion of water when swimming during the rainy season, particularly in the most polluted section, downstream of a large wholesale market. The estimated annual risks of diarrheal disease due to infection by the protozoan parasites were up to 120-fold greater than the reported disease incidence in the vicinity of the studied district and the entire Thailand, suggesting a significant host resistance to disease beyond our model's assumptions. In contrast, annual disease risk estimates for DEC were in agreement with actual cases of diarrhea in the study area.