Magnetotelluric (MT) measurements were made in southern Manitoba, Canada, as part of the Portable Observatories for Lithosphere Analysis and Research Investigating Seismicity (POLARIS) project, to image the northeastern part of the Williston basin and underlying Precambrian lithosphere. Data collected at 21 sites along a 400 km east–west profile at 49.5°N and a 300 km north–south profile at 100°W were analyzed using robust spectral analysis, tensor decomposition, and two-dimensional inversion. The resulting resistivity models allow subdivision of the Williston basin into three layers: an upper layer of 1–5 Ω·m corresponding to Mesozoic and upper Paleozoic rocks, a 20–50 Ω·m layer corresponding to lower Paleozoic carbonate rocks, and a 2–3 Ω·m layer corresponding to the Ordovician Winnipeg Formation. Deeper penetrating MT responses, interpreted with other MT data, reveal a region in the westernmost Superior craton with a southwest–northeast geoelectric fabric that is oblique to subprovince boundaries. The observations can be explained by Proterozoic deformation extending several hundred kilometres east of the Superior boundary zone or by a separate Archean terrane adjacent to the boundary. The Thompson belt (TOBE) conductor in the south of the study area has previously been interpreted as part of the Superior boundary zone (SBZ). However, MT results show that the conductor does not extend continuously along the margin of the zone and MT studies to the north define conductors on the margin of the Sask craton. The results suggest the TOBE conductor is associated with the Sask craton margin. The MT results indicate significant along-strike variation of the SBZ in southern Manitoba.