Conceptual models of the fracture networks in shale were evaluated at a site contaminated with chlorinated solvents. Prior borehole testing in eight holes under open hole ambient and pumping conditions identified 14 flow zones (140 m bedrock interval) with zero to five zones per hole. Cross-hole testing showed only a few cross-connections between transmissive fractures. The initial conceptual model thus featured a sparse fracture network with few dominant fractures. Detailed profiles (hydraulic head, rock core volatile organic compounds, groundwater volatile organic compounds from packer and multi-level sampling, cross-hole multi-level monitoring of permanganate injections) were collected from several holes and indicated a well-connected fracture network with many hydraulically active fractures not influenced by open hole cross-connection. This contrasting conceptual model contained numerous well-connected horizontal and vertical fractures that allowed chlorinated solvents to penetrate the upper 50–60 m of bedrock as dense non-aqueous phase liquids, followed by diffusion-driven mass transfer from fractures into the porous rock matrix, such that nearly all the contaminant mass resided as dissolved and sorbed phases, measurable in rock core without cross-contamination during drilling. The difference in the two conceptual models has important implications for source zone and plume attenuation.