Regional‐scale geologic structures characteristic of mantle lithosphere within cratons found in continent interiors are interpreted using geo‐registered diverse data sets from the Slave craton of northwest Canada. We developed and applied a new method for mapping seismic discontinuities in three dimensions using multiyear observations at sparse, individual broadband receivers. New, fully 3‐D conductivity models used all available magnetotelluric data. Discontinuity surfaces and conductivity models were geo‐registered with previously published P‐wave and surface‐wave velocity models to confirm first‐order structures such as a midlithosphere discontinuity. Our 3‐D model to 400 km depth was calibrated by “drill hole” observations derived from xenolith suites extracted from kimberlites. A number of new structural discontinuities emerge from direct comparison of coregistered data sets and models. Importantly, we distinguish primary mantle layers from secondary features related to younger metasomatism. Subhorizontal Slave craton layers with tapered, wedge‐shaped margins indicate construction of the craton core at 2.7 Ga by underthrusting and flat stacking of lithosphere. Mapping of conductivity and metasomatism in 3‐D, the latter inferred via mineral recrystallization and resetting of isotopic ages in xenoliths, indicates overprinting of the primary layered structures. The observed distribution of relatively conductive mantle at 100–200 km depths is consistent with pervasive metasomatism; vertical “chimneys” reaching to crustal depths in locations where kimberlites erupted or where Au mineralization is known. Key Points The craton was assembled by stacking of Archean lithospheric layers Craton margins are characterized by dipping discontinuities and wedge tectonics Metasomatized mantle is conductive and cross‐cuts constructional layers