The role of disease in freshwater mussel declines has been largely ignored due to the lack of appropriate diagnostic tools and metabolomic markers of stress. Mussels in this study were either fed a prepared diet or unfed and their condition was assessed with the observed changes in fatty acid content of their tissue. This dataset contains quantitative fatty acid data from nonlethal (biopsy) sampling of foot tissue. These data may provide biomarkers indicative of freshwater mussel’s metabolic status.