Where soils are shallow, effluents from on-site wastewater disposal systems (OSWDS) can be dispensed onto underlying weathered bedrock. Viruses contained in the effluents pose a threat to groundwater quality if the weathered bedrock materials do not possess the properties necessary to treat the effluents before they reach groundwater. The extent and pathways of water flow and virus transport in fractured, weathered granitic bedrock were investigated at a field site in southern California. A suspension containing MS-2 bacteriophage, sodium bromide, and blue dye was ponded at the soil–weathered bedrock interface and allowed to infiltrate for 9 h. A trench was excavated, and bedrock samples were collected and assayed for water, bromide, and MS-2 content. Distributions of dye, bromide, and MS-2 indicate that joint fractures facilitated the channeling of water and of viruses to depths >105 cm. Infiltration data suggest that fracture channeling occurred primarily during the first 50 min, after which time vertical convective flow through the bedrock matrix was the primary infiltration and transport process. The transition from fracture to matrix flow was the result of a decrease in fracture aperture caused by the swelling of pedogenic clay in the weathered bedrock matrix. Bromide and MS-2 concentration profiles suggest that the lower extent of matrix flow was 45 cm, below which water flow and virus transport occurred solely via fracture channeling. These results indicate that caution should be used when operating OSWDS on weathered granitic bedrock in California, and emphasize the need to collect morphologic and hydraulic data prior to their installation.