The proper management of fecal sludge (FS), to block the transmission pathways of pathogens, is rarely enforced in many parts of the world. Health risks associated with different disposal practices of FS in peri-urban settings of a large metropolis in Thailand were assessed; Tha Klong sub-district with indiscriminate FS dumping, and Klong Luang sub-district which has an FS treatment system. The study showed that indiscriminate FS dumping from along the canal banks and discharge of market waste were likely the major sources of E. coli and Salmonella spp. in contamination of the canal water. The increased microbial pathogen concentrations near the FS treatment facility also indicated contamination risks from poorly designed treatment facilities. Quantitative microbial risk assessment (QMRA) indicated very high water-related infection risk levels compared to the actual locally recorded disease occurrences. These results indicated that the QMRA model needs to be modified to take account of immunological differences between populations in developed countries, where the model was developed, and developing countries. In addition, further sensitivity factors are needed to reflect different societal behavior patterns, and therefore contact with potentially contaminated water, in different sub-populations of many less developed communities.