The southern arrow squid, Nototodarus sloanii (Ommastrephidae), is a key species in New Zealand’s pelagic ecosystem and is commercially fished. Specimens in this study were caught along the Chatham Rise—one of New Zealand’s most heavily targeted fisheries areas. Nine different tissue types were analysed from 15 female and 15 male specimens for 13 trace elements (As, Cd, Co, Cr, Cu, Fe, Hg, Ni, Mn, Pb, Sb, V, and Zn). Trace element concentrations varied among tissue types with the highest concentrations observed in the digestive gland, the branchial hearts, and the kidney. The mean observed concentrations of As, Cd, Hg, and Pb in the muscular tissues were less than their respective maximum permissible levels for seafood consumption for adults. However, analysis of market squid showed that Cd contamination from the digestive gland to the mantle tissue occurs and can potentially pose a threat to human consumers. We recommend regular testing of the potential exposure of Cd in human diets.