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Pathogen management in agriculture has become an important environmental and health issue, especially as it relates to water quality. Drainage water and surface runoff water are potential sources for pathogen entry into the environment from fields treated with manure. As well, leachate from animal mortality and compost management facilities can be a potential source of pathogen contamination in both ground and surface water. By indirectly monitoring for pathogens using indicator bacteria like Escherichia coli, the levels of these organisms that are associated with agricultural practices can be determined and better management practices can be developed that reduce environmental risks. This paper will outline the E. coli monitoring system that is in place in Nova Scotia, Canada.