Boreholes drilled through contaminated zones in fractured rock create the potential for vertical movement of contaminated ground water between fractures. The usual assumption is that purging eliminates cross contamination; however, the results of a field study conducted in a trichloroethylene (TCE) plume in fractured sandstone with a mean matrix porosity of 13% demonstrates that matrix‐diffusion effects can be strong and persistent. A deep borehole was drilled to 110 m below ground surface (mbgs) near a shallow bedrock well containing high TCE concentrations. The borehole was cored continuously to collect closely spaced samples of rock for analysis of TCE concentrations. Geophysical logging and flowmetering were conducted in the open borehole, and a removable multilevel monitoring system was installed to provide hydraulic‐head and ground water samples from discrete fracture zones. The borehole was later reamed to complete a well screened from 89 to 100 mbgs; persistent TCE concentrations at this depth ranged from 2100 to 33,000 μg/L. Rock‐core analyses, combined with the other types of borehole information, show that nearly all of this deep contamination was due to the lingering effects of the downward flow of dissolved TCE from shallower depths during the few days of open‐hole conditions that existed prior to installation of the multilevel system. This study demonstrates that transfer of contaminant mass to the matrix by diffusion can cause severe cross contamination effects in sedimentary rocks, but these effects generally are not identified from information normally obtained in fractured‐rock investigations, resulting in potential misinterpretation of site conditions.