An outbreak of hepatitis E virus (HEV) began in October 2007 in northern Uganda. To determine risk factors and sources for ongoing transmission, we conducted both a case-control study and an environmental investigation. A case patient was defined as having serologic evidence of HEV infection, whereas controls were seronegative. We identified risk factors for infection by univariable and multivariable analyses using conditional logistic regression. Several water sources were tested for HEV RNA. Among 112 cases and 145 controls, storage of drinking water in large-mouthed vessels (adjusted odds ratios [AOR] = 2.83; 95% confidence interval [CI] = 1.16-6.94) and washing hands in a group basin (AOR = 1.90; 95% CI = 1.07-3.38) were associated with HEV infection. HEV RNA was detected from communal hand-rinse and surface-water samples. The epidemiologic and environmental water-testing results suggest that household-level factors played an important role in the transmission of HEV-modalities that have been previously underappreciated.