The Silverton caldera in southwest Colorado, USA hosts polymetallic veins and pervasively altered rocks indicative of porphyry copper systems. Nearly a kilometer of erosion has exposed multiple levels of the hydrothermal systems from shallow lithocaps down to quartz-sericite-pyrite veins. New airborne electromagnetic and magnetic survey data are integrated with previous alteration mapping and porphyry models to show the subsurface geophysical response of shallow to deep levels of the porphyry system. Qualitative map views show lateral changes in the magnetization and resistivity of the hydrothermally altered rocks. The volcanic terrain exhibits high magnetization and high amplitude anomalies map near-surface plutonic rocks associated with porphyry systems. Magnetic susceptibility measurements on outcrops of hydrothermally altered rocks indicate magnetite content decreases upward and outward from the source intrusions where magnetic anomaly lows are observed over the lithocaps. The resistivity maps highlight hydrothermal alteration as resistivity lows with exception being rocks having propylitic alteration. Quantitative resistivity models show low resistivity zones with an apparent thickness around 50–150 m beneath quartz-sericite-pyrite veins interpreted to be the result of supergene processes that may continue today, and the calculated magnetic source depths occur near the top of this zone. The resistivity models also show rocks having propylitic, silicic, and quartz-alunite-pyrophyllite assemblages exhibit high resistivity with depth, and argillic alteration assemblages had high resistivity due to high quartz content. This integrated approach presented in a three-dimensional environment provides guidance when exploring for porphyry copper systems in less exposed terrains.