There is an increasing need to image the shallow (top 100 m) subsurface using geophysical techniques to inform resource use, resource protection, regulatory and policy development, community resilience, and, in general, how humans can live and interact with their environment. Geothermal systems are one such natural resource whose shallow hydrological structures are generally poorly understood, yet extensively utilised. Understanding the geothermal hydrology will inform potential environmental effects and the hydrothermal risk. The towed transient electromagnetic (tTEM) geophysical technique has been successfully applied to map permeability structures associated with current and/or historical near-surface geothermal flow and/or hydrothermal alteration in parts of the Rotorua and Wairakei-Tauhara Geothermal Fields, New Zealand. High-density tTEM measurements have enabled distinctive near-surface (top 100 m) resistivity anomalies to be identified and be interpreted. Large-scale resistivity anomalies that have been interpreted in this study include geothermal alteration associated with ascending boiling geothermal fluids, lateral near-surface permeable zones, and potential locations of aquifers that feed geothermal springs. Additional information is generally needed to differentiate between these potential causes of low resistivity anomalies. Contrasts in the modelled resistivities are stronger over “up-flow” areas (areas where near-boiling chloride-type water is rising close to the ground surface) compared to steam-heated geothermal areas. This is likely caused by vigorous processes (such as might be expected at the fluid-boiling interface) acting on the capping rock in the up-flow areas making the tTEM technique valuable in identifying potential fluid pathways from depth to the surface in these areas. New insights into the shallow permeability structure with possible near-surface boiling zones are located at 50 m below the ground at one of the study sites. Identification of these areas not only help understand how geothermal fluid moves from depth to the surface but can also contribute to managing the hydrothermal explosion hazard in these areas.