Discoveries from multi-beam sonar mapping and seismic reflection surveys of the northern, central, and West Thumb basins of Yellowstone Lake provide new insight into the extent of post-collapse volcanism and active hydrothermal processes occurring in a large lake environment above a large magma chamber. Yellowstone Lake has an irregular bottom covered with dozens of features directly related to hydrothermal, tectonic, volcanic, and sedimentary processes. Detailed bathymetric, seismic reflection, and magnetic evidence reveals that rhyolitic lava flows underlie much of Yellowstone Lake and exert fundamental control on lake bathymetry and localization of hydrothermal activity. Many previously unknown features have been identified and include over 250 hydrothermal vents, several very large (>500 m diameter) hydrothermal explosion craters, many small hydrothermal vent craters (∼1–200 m diameter), domed lacustrine sediments related to hydrothermal activity, elongate fissures cutting post-glacial sediments, siliceous hydrothermal spire structures, sublacustrine landslide deposits, submerged former shorelines, and a recently active graben. Sampling and observations with a submersible remotely operated vehicle confirm and extend our understanding of the identified features. Faults, fissures, hydrothermally inflated domal structures, hydrothermal explosion craters, and sublacustrine landslides constitute potentially significant geologic hazards. Toxic elements derived from hydrothermal processes also may significantly affect the Yellowstone ecosystem.