We mapped the geometry of a shallow confining layer within the Salinas Valley aquifer system, northern Monterey County, California, using indicator geostatistics. The confining layer was previously interpreted to be mainly Holocene in age, having been deposited as a single unit during post-Wisconsin sea-level rise. We interpret this layer in our field area to be associated with Isotope Stages 5 (84--121 kyr) based on three independent arguments: layer geometry, with three distinct clay units rather than one; 14C analyses of peat samples; and consideration of required rates of coastal uplift. The complex stratigraphy of the confining layer likely resulted from deposition over existing topography, erosion during exposure, and uplift during three intervals of sea level rise and fall. Similarly complex layering may occur in other coastal basins, influencing groundwater resource development, remediation and protection in these settings.