The Common Carp Cyprinus carpio is an invasive fish whose populations have grown to ecologically damaging levels in the North American Midwest. It has been shown that some shallow nursery habitats contribute disproportionally to population growth of Common Carp in interconnected Midwestern lake systems. The ability of managers to discriminate which shallow basins are producing Common Carp across these systems could increase the efficacy of management practices aimed at disrupting recruitment. We tested whether adult and juvenile Common Carp collected across an interconnected Midwestern lake system could be distinguished based on the concentrations of 11 trace elements measured in their otoliths using laser ablation and high-resolution inductively coupled plasma mass spectrometry (n = 157). Elemental concentrations in water were also measured with inductively coupled plasma mass spectrometry and found to differ among sites and between habitats, indicating that variation in otolith microchemistry was likely. Aluminum, barium, copper, iron, potassium, lithium, magnesium, sodium, phosphorus, and strontium in the edge region of otoliths differed significantly among Common Carp from all capture sites. Barium, iron, lithium, manganese, and phosphorus differed significantly among juvenile Common Carp from three nursery basins. Aluminum, barium, copper, iron, potassium, lithium, sodium, phosphorus, and strontium were significantly different between nursery and nonnursery habitats. We then investigated the ability to use these elemental otolith edge signatures to differentiate capture locations and distinguish between locations that are active and putative nursery habitats. Quadratic discriminant analysis could classify otoliths to collection site with an accuracy of 54%. Quadratic discriminant analysis had increased accuracy when restricted to juvenile Common Carp (76%) and when classifying Common Carp to nursery and nonnursery habitat types (87%). Further analysis of otolith and water microchemistry indicates temporal instability and suggests a need to collect a multiyear library of otoliths prior to utilization by managers.