Brown stains sometimes appear in the inner shell layers (nacre) of freshwater mussels. An electron microprobe was used to analyze the stained nacre of the unionid Amblema plicata (Say, 1817) from selected localities on the Mississippi River in the vicinity of Lacrosse and Prairie du Chien, Wisconsin.Several elements such as Na, Mg, Al, Si, P, S, C1, K, and Fe are more highly concentrated in stained than in unstained nacre. Concentrations of these elements relative to Ca were found to vary significantly among the localities from which the specimens were obtained. Ratios have significantly higher variances downstream of the confluence of the Yellow and Mississippi Rivers, downstream of a barge fleeting area, near the town of Marquette, Iowa, near the site of sewage effluent for Prairie du Chien, Wisconsin and downstream of a scrap metal yard near Lacrosse, Wisconsin in contrast to control localities.Suspended silt, the result of runoff and river activity (barge traffic, dredging, pleasure boating) may be the stimulus for stain formation. Clay minerals adsorb accessory elements and in turbid water are trapped within the pallial space of A. plicata. The mussel secretes an organic-rich, periostracum-like layer over the entrapped sediment, and later reverts to prismatic and finally nacreous shell deposition. Some of the elements found in the stain could directly disturb Ca metabolism by competing with Ca for binding sites in shell aragonite.