Aeromagnetic data helped us to understand the 3D distribution of plutonic rocks near the Pebble porphyry copper deposit in southwestern Alaska, USA. Magnetic susceptibility measurements showed that rocks in the Pebble district are more magnetic than rocks of comparable compositions in the Pike Creek–Stuyahok Hills volcano-plutonic complex. The reduced-to-pole transformation of the aeromagnetic data demonstrated that the older rocks in the Pebble district produce strong magnetic anomaly highs. The tilt derivative transformation highlighted northeast-trending lineaments attributed to Tertiary volcanic rocks. Multiscale edge detection delineated near-surface magnetic sources that are mostly outward dipping and coalesce at depth in the Pebble district. The total horizontal gradient of the 10-km upward-continued magnetic data showed an oval, deep magnetic contact along which porphyry deposits occur. Forward and inverse magnetic modeling showed that the magnetic rocks in the Pebble district extend to depths greater than 9 km. Magnetic inversion was constrained by a near-surface, 3D geologic model that is attributed with measured magnetic susceptibilities from various rock types in the region. The inversion results indicated that several near-surface magnetic sources with moderate susceptibilities converge with depth into magnetic bodies with higher susceptibilities. This deep magnetic source appeared to rise toward the surface in several areas. An isosurface value of 0.02 SI was used to depict the magnetic contact between outcropping granodiorite and nonmagnetic sedimentary host rocks. The contact was shown to be outward dipping. At depths around 5 km, nearly the entire model exceeded the isosurface value indicating the limits of nonmagnetic host material. The inversion results showed the presence of a relatively deep, northeast-trending magnetic low that parallels lineaments mapped by the tilt derivative. This deep low represents a strand of the Lake Clark fault.