A multiscale magnetic survey of the northern basin of Yellowstone Lake was undertaken in 2016 as part of the Hydrothermal Dynamics of Yellowstone Lake Project (HD-YLAKE)-a broad research effort to characterize the cause-and-effect relationships between geologic and environmental processes and hydrothermal activity on the lake floor. The magnetic survey includes lake surface, regional aeromagnetic, and near-bottom autonomous underwater vehicle (AUV) data. The study reveals a strong contrast between the northeastern lake basin, characterized by a regional magnetic low punctuated by stronger local magnetic lows, many of which host hydrothermal vent activity, and the northwestern lake basin with higher-amplitude magnetic anomalies and no obvious hydrothermal activity or punctuated magnetic lows. The boundary between these two regions is marked by a steep gradient in heat flow and magnetic values, likely reflecting a significant structure within the currently active~20-km-long Eagle Bay-Lake Hotel fault zone that may be related to the~2.08-Ma Huckleberry Ridge caldera rim. Modeling suggests that the broad northeastern magnetic low reflects both a shallower Curie isotherm and widespread hydrothermal activity that has demagnetized the rock. Along the western lake shoreline are sinuous-shaped, high-amplitude magnetic anomaly highs, interpreted as lava flow fronts of upper units of the West Thumb rhyolite. The AUV magnetic survey shows decreased magnetization at the periphery of the active Deep Hole hydrothermal vent. We postulate that lower magnetization in the outer zone results from enhanced hydrothermal alteration of rhyolite by hydrothermal condensates while the vapor-dominated center of the vent is less altered. Plain Language Summary Despite many previous investigations, uncertainties remain about the circulation of hot fluids and gas below the floor of Yellowstone Lake. In this study, we use measurements of the strength of the magnetic field at different heights above the lake floor (via plane, helicopter, boat, and autonomous submersible) to study the rock magnetization, which is a physical property caused by the presence of magnetic minerals. Magnetization varies with rock type, temperature, and hydrothermal alteration of the rock. Our results show that rocks beneath the northeastern part of the lake are less magnetized because of higher temperatures at depth and intense and widespread circulation of hot fluids in the lake floor that destroys magnetic minerals in the rock. In contrast, stronger magnetization beneath the northwestern lake basin suggests that volcanic rocks are unaltered because of lower temperatures and the absence of similar hot fluid circulation at depth. Our measurements allow us to observe structures in the subsurface that might be paths or barriers to fluids. The submersible measurements acquired near the lake floor show decreased rock magnetization at the periphery of a hot gas venting area, where mixing with lower-temperature waters allows the gas to condense and efficiently alter the rock.