This paper summarizes the results of a study to evaluate the applicability of pathogen surrogates to be used by treatment plant operators as a tool in continuous plant performance optimization. The target pathogens were Giardia, Cryptosporidium, and enteric viruses. Pathogen surrogates were selected among indigenous, non-pathogenic microorganisms that represent the target pathogens in removal through treatment. The selected surrogate could then become a tool to integrate source water quality information with treatment plant operations. The implementation of a representative surrogate as a monitoring and operational tool should improve overall treatment process reliability and provide a sound basis for reducing the likelihood of microbial pathogen breakthrough. The study was conducted using operating water treatment facilities and routine monitoring procedures supplemented by specific microbial analyses conducted at a single laboratory. A comprehensive matrix was developed to relate water quality and process variables using 22 surface water treatment facilities and one unfiltered source as test sites.