Chemical risk assessments often focus on measuring exposure as if individuals were subject only to exogenous environmental sources of risk. For infectious diseases, exposure might not only depend on exogenous sources of microbes, but also on the infection status of other individuals in the population. For example, waterborne infections from agents such as Cryptosporidium parvum and Escherichia coli: O157:H7 might be transmitted from contaminated water to humans through drinking water; from interpersonal contact; or from infected individuals to the environment, and back to other susceptible individuals. These multiple pathways and the dependency of exposure on the prevalence of infection in a population suggest that epidemiological models are required to complement standard risk assessments in order to quantify the risk of infection. This paper presents new models of infection transmission systems that are being developed for the US Environmental Protection Agency as part of a project to quantify the risk of microbial infection. The models are designed to help inform water treatment system design decisions.