The formation of granitoids, predominantly tonalite-trondhjemite-granodiorite (TTG) suites was a key process in the differentiation of Earth’s earliest crust. However, the relative importance of intracrustal reworking versus input from external sources remains unclear. U–Pb and Hf isotopic data collected from zircon in Archean granitoids frequently support reworking and partial melting of a common crustal reservoir over time to produce subsequent generations of melt. A less frequently observed isotopic signature, in a single region, implies the production of different generations of TTGs from unrelated sources. These end-member scenarios of granitoid generation have quite different implications for Archean crustal evolution. Here, we investigate TTGs from across a crustal cross-section known as the Kapuskasing Uplift in the Neoarchean Wawa terrane of the southern Superior Province. We report U–Pb and Hf isotopic data from zircon in TTGs from the lower, middle, and upper crust to evaluate their sources. Results indicate three groups of TTGs: a ca. 2885 Ma upper-crustal TTG with chondritic εHf, ca. 2835–2820 Ma lower-crustal TTGs with subchondritic εHf, and ca. 2750–2685 Ma TTGs with suprachondritic εHf emplaced at middle- to upper-crustal levels. Each group was derived from an isotopically distinct source. We propose that the Mesoarchean rocks exposed in the Kapuskasing Uplift represent a crustal fragment rifted from the margin of existing Mesoarchean terranes in the Superior Province. Subsequent Neoarchean juvenile magmatism dominates the upper and middle crust resulting in isotopic stratification of the Kapuskasing Uplift, as only the lower crust contains evidence of all three isotopic sources. Inferences about Archean crustal evolution in general rely on upper- to middle-crustal rocks (i.e., greenstone belts and grey gneiss), as these represent the majority of exposed Archean crust worldwide. The potential for the lower crust to be decoupled from overlying rocks implies that some parts of the Archean geological record may be preserved only at the deepest crustal levels—particularly rocks related to the most ancient sources.