Exploration for unconformity-associated uranium deposits requires detailed 3D knowledge of the depth and morphology of the unconformity surface. Modifications of the unconformity surface by reactivated intersecting faults and favorable basement lithology are key parameters when attempting to vector toward potential deposits. In the absence of seismic reflection and closely spaced drill data, high-resolution aeromagnetic data can provide surprisingly detailed 3D constraints through the use of source depth routines. Such routines are applied to the northeastern part of the Thelon Basin, termed the Aberdeen Subbasin, in Nunavut. This region is considered prospective for unconformity-associated uranium deposits. Deposits have so far been discovered adjacent to the subbasin where they are hosted by structurally complex Neoarchean and early Paleoproterozoic supracrustal rocks. We determined the morphology of two unconformity surfaces by combining the outputs from multiple analyses of high-resolution aeromagnetic data: three semiautomated depth estimation routines (Werner deconvolution, Euler deconvolution, and source parameter imaging) and two potential field inversion procedures. Confidence in depth estimates was increased by combining the output of individual source depth algorithms. Results were integrated with previously mapped fault displacements, seismic refraction profiles, boreholes, and outcrop geology around the subbasin perimeter. An integrated pseudo-3D source depth estimate of the unconformity surface is presented as twenty-three north–south profiles. The revised model of the upper unconformity surface, the base of the Thelon Formation, shows a complex set of stepped blocks bounded by four major intersecting fault arrays with approximate offsets ranging from tens to hundreds of meters.