Estonia's Mesoproterozoic (∼1.6 Ga) Rapakivi intrusions are hosted within a structurally complex Precambrian basement influenced by the Paldiski-Pskov Deformation Zone (PPDZ) and are largely concealed beneath Phanerozoic sedimentary cover. Their subsurface geometries, depth extents, and structural relationships remain incompletely constrained. We investigated the Märjamaa-Kloostri, Naissaare, and Neeme intrusions to a model depth of ∼15 km using gravity and magnetic data, spectral filtering, potential-field derivatives, upward continuation, and three-dimensional joint inversion with SimPEG. Regional gravity and magnetic gradients broadly follow the NW-SE orientation of the PPDZ, whereas the recovered density-contrast and magnetic-susceptibility models reveal distinct subsurface architectures. Märjamaa exhibits a shallow concentric geometry consistent with piston-cauldron emplacement, underlain by heterogeneous, vertically organised geophysical domains extending below the depth investigated in previous local-scale models. Kloostri Phase III displays a comparatively tabular geometry adjacent to the northeastern margin of Märjamaa Phase II. Naissaare exhibits a vertically extensive magnetic structure partly offset from shallower, heterogeneous density domains, potentially reflecting deeper intrusive or magma-transfer components. Neeme produces weaker geophysical contrasts, combining a shallow density body with deeper, laterally displaced magnetic anomalies. The correspondence between recovered geophysical domains and mapped magmatic phases varies among the intrusions, highlighting differences in their internal petrophysical architecture. Although their regional setting is associated with the PPDZ, the inversion does not resolve continuous subsurface connections between the three intrusive systems. These findings suggest that the Estonian Rapakivi intrusions developed within a shared tectonomagmatic framework while preserving distinct subsurface geometries and physical-property distributions, potentially reflecting differences in magma emplacement, structural accommodation, and local crustal conditions.