Calculating Cryptosporidium inactivation throughout the water treatment process as a function of chlorine dioxide concentration and contact time, as is current practice, requires a good understanding of the hydraulics of the process. This study investigated the use of a novel approach whereby Cryptosporidium inactivation levels were calculated using actual measured inactivation levels of a surrogate microorganism across the disinfection process. A survey of aerobic and anaerobic bacterial spores in waters from various sites across North America where chlorine dioxide (and/or chlorine) is utilized was conducted. Spore concentrations were measured in natural waters as well as throughout water treatment process. Predominant environmental isolates that survived disinfection were identified, cultured in the laboratory, and their inactivation kinetics in bench-scale experiments investigated. To date, spore inactivation rates have been measured for six full-scale facilities from Canada and USA. Two hundred and twelve spore-forming bacteria have been isolated so far from environmental isolates. Most of the aerobic spore-forming bacteria are of the genus Bacillus, whereas most of the anaerobic-spore forming bacteria are of the genus Clostridium. Strains were identified at the species level using the Biolog(R) system. Certain aerobic spore-forming isolates were common to several utilities. They were identified and were found to belong to six species: B. pumilus; B. amyloliquefaciens; B. cereus/thuringiensis; B. halodurans; B. licheniformis; and, B. subtilis. The chlorine dioxide inactivation kinetics of these bacteria were tested and found to vary significantly. Includes 15 references, tables.