Clays are Mother Nature's "metal magnet." In the sedimentary record, after the sands and limestones are sorted out, the clay layers collect the leftover impurities that often include metals and trace elements. As you already know, some formations have relatively no clay or clay layers, or clays may appear ubiquitously (evenly) distributed throughout the formation.
A problem arises when there may truly be a site metal contaminant such as lead, which is both naturally occurring and a contaminant. In this case, background or upgradient samples should be collected to determine naturally occurring levels. This level then should be subtracted from the site sample concentrations to determine the amount above the background level.
In summary, when sampling for metals, follow the required sampling protocol, but try to obtain the clearest, non-turbid water sample as possible.