The northeast Thelon Basin in the Kivalliq region of Nunavut is prospective for uranium deposits. Recently discovered basement-hosted, unconformity-associated prospects west of Kiggavik are restricted to deformed and metamorphosed Neoarchean psammitic enclaves of the Woodburn Lake group within 1.83 Ga Hudson granite and Martell syenite that together comprise the Shultz Lake intrusive complex (SLIC). The depth and geometry of the intrusive complex are relatively unknown as the geological constraints are poor; the drilling is sparse and of shallow depth extent as it was not targeting the basement but shallower multiply faulted and highly altered demagnetized zones. This study aims to constrain the geometry and context of the Shultz Lake intrusive complex with respect to the ore-hosting Neoarchean metasedimentary rocks and intersecting reactivated fault arrays through geophysical modelling of detailed aeromagnetic and gravity data integrated with new geological knowledge. By integrating detailed gravity, aeromagnetic, and structural geology observations measured along a series of transects with a petrophysical rock properties database, it is possible to derive constraints on the depth and thickness (200–300 m) of the SLIC. Quantitative comparison and integration of multiple hypothetical geometries favours a model wherein the SLIC, together with metasedimentary and older basement gneiss, has been structurally emplaced over the Neoarchean metasediments.