Mussels are an indicator species for water quality due to exposure to acute water pollutants from their filter feeding life style (Augspurger 2003). Mussels are also more susceptible to trace metal exposure than many other aquatic organisms due to their behavior of burrowing in fine grained sediments and feeding on detritus and particulate matter (Wilson 2008). Metal accumulation is proportional to the assimilation efficiency of metals from food (Wang and Fisher 1999) and through the examination of waters and sediments in which these organisms live insight into potential effects posed by harmful trace metals can be identified. Since 1993, the Appalachian elktoe (Alasmidonta raveneliana) has been federally listed as a critically endangered species. An area of high population density for the elktoe mussel was the Upper Little Tennessee River. In 2006 biologists began to notice a severe decline in the elktoe population during routine mussel monitoring surveys. In order to understand the water quality threats posed to elktoe mussels, water quality parameters were monitored during this project. From January 2009–January 2010, HACH water quality sondes were deployed at three monitoring sites along the Upper Little Tennessee River to evaluate the aquatic habitat and determine surface water quality. Analyses of water samples and shell material for selected trace metals were conducted using an ICP-MS. Temporal variations of total suspended sediment loads during floods were also documented at these sites. Further observation into the presence of copper was accomplished through porewater sampling along the reach of the Upper Little Tennessee River known to currently contain elktoe mussel populations. Although other studies have found trace metal concentrations of barium, chromium, nickel, lead and zinc in sediment well above probable effect thresholds, the portion of these trace metals found in bioavailable concentrations appears to be low on the basis of shell and copper data from porewater investigations. Copper levels did show wide local variability, suggesting that levels are significantly different on a localized scale. Moreover, the porewater samples were collected from September 2010 to January 2011, and therefore do not account for high inputs of common local fertilizers and/or significant changes in temperature and pH in the warmer seasons. Copper and zinc levels in the water column rose significantly during storm events observed during this project posing a potential threat to elktoe mussels. Specific threats include elevated sediment transport rates leading to increased turbidity and enhanced trace metal loads during rainfall events. Sediments also could be reworked from upstream impoundments during high water events, such as the back to back hurricanes of 2004 after which the mussel declines were noticed. These observations are consistent with other studies that have found high concentrations of trace metals, including copper and zinc, in sediments of Lake Emory and the Little Tennessee River that locally exceed probable effect thresholds for aquatic biota. Thus, trace metal-rich sediments located at the upstream terminus of the elktoe mussel habitat appears to pose a significant threat to mussel populations.