Magmatic and metamorphic processes modifying the lower crust and uppermost mantle are key to understanding continental growth and evolution. However, our ability to identify and quantify such processes is challenged by inaccessibility, data sparsity, and uncertainties in defining properties at depth. As a result, knowledge of composition, metamorphic grade, and the nature of the continental crust-mantle transition is often limited. Here, we model the structure and properties of the crust and uppermost mantle between the West and North Australian Cratons to infer tectonic processes at this major lithospheric boundary. Seismically constrained 3D gravity inversions were used to estimate crustal and mantle densities and Moho depths. The application of isostatic principles and the joint interpretation of gravity, active and passive seismic models, well data, and outcrop data are used to identify and characterize anomalous masses that are otherwise unresolvable using supracrustal datasets. The results suggest a thick, dense crust with a mafic bulk composition, a high-density, reflective lower crust, and a low-density uppermost mantle beneath the southern Canning Basin. We interpret these crustal and mantle features as reflecting mafic mantle-derived magmatism and crustal anatexis related to Proterozoic-Cambrian Large Igneous Provinces. In contrast, the Proterozoic Paterson Orogen exhibits a thick, dense, high-grade metamorphic bulk crust with a felsic to intermediate composition, a high-density, low-reflectivity lower crust, and low-density uppermost mantle, inferred to result from convergent tectonics. The northern Canning Basin displays a thinner, less dense crust with an intermediate to mafic composition, and mafic, high-density, reflective lower crust, associated with mafic magma emplacement during rifting and passive margin formation. These variations in crustal structure reveal a complex interplay of Proterozoic terrane amalgamation to the cratonic margin, repeated intraplate high-volume mafic magmatic events, and rifting of the offshore basin, which have collectively shaped the deep crust and uppermost mantle in this region.