Secondary structures (e.g., fractures, sand lenses, kimberlite intrusions) can compromise the ability of clay-rich bedrock aquitards to protect underlying aquifers from near-surface contamination. To date, the effects of secondary structures on water migration and solute transport in these deposits have been poorly characterized. This study characterized the water migration and solute transport mechanisms at both a geologically simple and a geologically complex late-Cretaceous shale aquitard, with the field sites located 5 km apart in central Saskatchewan, Canada. The geotechnical properties and hydrogeologic properties of the complex aquitard were altered by kimberlite volcanism and subsequent hydrothermal alteration during its deposition (99 to 112 Ma BP). High-resolution, 1-D vertical profiles of conservative δ2H and Cl were collected from both sites (203 and 353 m deep, respectively) to define the vertical solute transport mechanisms. The shape of the 1-D tracer profiles and associated solute transport modeling from the geologically simple site suggest diffusion is the dominant transport mechanism through the entire thickness of the Lower Colorado shale aquitard (330 to 246 m above sea level, asl). Similarly, profiles through the complex, fractured, Cretaceous shale and associated modeling suggest diffusion is the dominant transport mechanism through the entire profile despite the presence of fractures; however, hydrothermal alteration during cooling of the kimberlite volcaniclastic material reduce the effective porosity (ne) of the kimberlite material from 40% to 1-5%. Results also suggest that, despite kimberlite emplacement in the study area, water migration and solute transport in the overlying and underlying Cretaceous shale may be unaffected by kimberlite volcanism and associated fracturing and alteration.