Lineament identification is a standard but controversial hydrogeologic practice. In this study, we present a rigorous examination of the hydrology of lineaments in a crystalline bedrock setting. Lineaments are reinterpreted as watershed-scale hydraulic barriers, in contrast to previous interpretations as fractured conduits that focus recharge and flow. In the study area, an ~900 km2 watershed underlain by the granitic and gneissic terrain of the Canadian Shield, bedrock lineaments are associated with linear lake shores and perennial wetland complexes. Lineaments were identified using a robust multi-image method and characterized by remote sensing, fracture mapping, drilling, hydraulic characterization, and numerical simulation of a coupled groundwater–surface-water system. Results indicate that two principal lineament sets are oriented parallel to fracture and fault orientations, and thus lineaments are interpreted as structural features, either fault zones or fracture zones with limited displacement. Faulted lineaments are more effectively identified by digital elevation model (DEM) topographic data rather than Landsat tonal imagery. Hydrogeological characterization and geomatic data indicate that the fractured bedrock underlying lineaments is composed of poorly connected zones of reduced permeability due to fault zone and/or fluid flow processes. Field data and numerical simulations suggest that lineament areas are barriers to recharge and flow in this setting as a result of permeability reduction. Integrated data sets and models of lineament permeability that are geologically realistic result in a better understanding of fractured bedrock aquifers and patterns of fluid flow in the brittle uppermost crust.