Hydrothermal systems in Yellowstone National Park originate at shallow reservoirs and manifest on the surface along faults and fractures. Structural interpretation in Yellowstone’s hydrothermal basins is problematic due to intense alteration of the rock, widespread glacial deposits, and much of the structure being covered by Pleistocene rhyolite flows. To address this problem, magnetic gradients from vertical faults and horizontal stratum sources were compared to hydrothermal surface manifestations and random generated data as proxy locations for zone of high fracture permeability. Two-dimensional Kernel Density Estimates of random and observed distributions, based on the Euclidian distance between magnetic source and surface manifestations, align from vapor-dominated to water-dominated hydrothermal systems when ordered from low hydrothermal density and low fracture permeability to high hydrothermal density and high fracture permeability. Three-dimensional Kernel Density Estimate distributions were created using Euclidian geometry between estimated source depths of vertical and horizontal stratum and show multimodality of the distributions and are interpreted as zones of fractures and faults. Structural trends of magnetic gradients correspond to structural domains of the Yellowstone Plateau. The Snake River Plain structural domain is a prominent trend in all magnetic gradient analysis.