The subcellular partitioning of trace elements (TEs) may depend on their binding preferences, although few field data are available from mining-impacted areas. Northern pike and lake whitefish were collected from different aquatic systems located in the Yellowknife mining area (Northwest Territories, Canada) to examine the subcellular partitioning of TEs in liver cells. Elements belonging to metal classes based on binding affinities were considered: A (Ce, La), borderline (As, Pb), and class B (Ag, Cd). Measurements in the metal-detoxified fractions (granule-like structures and heat-stable proteins and peptides) and in the putative metal-sensitive fractions (heat-denatured proteins, mitochondria and microsomes, and lysosomes) revealed marked differences among metal classes. In both fish species, Cd and Ag accumulated more as detoxified forms (higher than 50%, likely bound to metallothionein-like proteins) than La and Ce (not more than 20%). The two borderline TEs (As and Pb) showed an intermediate behavior between classes A and B. Similar proportions were found in the “sensitive” subcellular fractions for all TEs, where quantitative ion character-activity relationships (QICARs) indicated the covalent index and electronegativity as predictors of the TE contribution in this compartment. This study supports the use of classes of metals to predict the toxicological risk of data-poor metals in mining areas.