In this paper, mathematical models are used to study the effects of both environmental conditions and malaria on Hepatitis E infections. The models designed are fit to data from the Kitgum outbreak, to estimate the basic reproduction number and to relate them to the level of contamination of the environment. We assume that the small number of latrines [23] , leads to contamination of environment. This in turn leads to contaminated water. Owing to the few number of bore holes in the region, lack of access to clean water gives rise to the viral infection of Hepatitis E.