The interaction between Cd and Zn in aquatic organisms is known to be highly variable. The purpose of this study was to use a subcellular compartmentalization approach to examine Cd and Zn interactions in the deposit-feeding polychaete Capitella capitata (sp. I). Laboratory-reared C. capitata were co-exposed to Cd (background or 50 μg Cd l−1) and Zn (background or 86 μg Zn l−1) with 109Cd and 65Zn as radiotracers for 1 week. After the 1-week uptake period, subsets of worms were allowed to depurate accumulated metals for an additional 1 week. Worms from both phases (uptake and loss) were then subjected to subcellular fractionation to determine the compartmentalization of metals as metal-sensitive fractions [MSF — organelles and heat-denaturable proteins (HDP)] and biologically detoxified metals [BDM — heat-stable proteins (HSP) and metal-rich granules (MRG)]. Uptake and loss of Cd and Zn in C. capitata at the whole body level were similar at bkgd-Cd/bkgd-Zn, with worms depurating the majority of accumulated metal (∼75% Cd and ∼64% Zn). When exposure of Zn or Cd was increased (bkgd-Cd/86-Zn; bkgd-Zn/50-Cd), uptake of background levels of Cd or Zn, respectively, was suppressed by ∼50%. These accumulated metals, however, were retained during the loss phase resulting in ∼40–50% greater Cd and Zn whole body tissue burdens than those of bkgd-Cd/bkgd-Zn worms. Beyond exhibiting similar patterns of uptake and loss at the whole body level, Cd and Zn behaved similarly at the subcellular level. Under background levels (bkgd-Cd/bkgd-Zn), after uptake, worms partitioned a majority of Cd (∼65%) and Zn (∼55%) to the HSP and organelles fractions. The HDP and MRG fractions contained less than ∼6% of both metals. Following depuration, at bkgd-Cd/bkgd-Zn, Cd and Zn were lost from all subcellular fractions; loss from HSP was the greatest contributor to whole body loss. When exposed to elevated concentrations of Zn or Cd, the suppression in uptake of bkgd-Cd or bkgd-Zn observed in whole body uptake was largely due to suppressions in the storage of Cd and Zn to HSP. These results suggest that Cd–Zn interactions reduce partitioning of both Cd and Zn to HSP, indicating that metal-binding proteins such as metallothioneins play a key role in these interactions.