Water-covered areas may lead to gaps in surface electromagnetic surveys, causing reduced resolution and, as a consequence, increased uncertainty in derived subsurface models. We have evaluated a boat-towed floating central loop time-domain electromagnetic technique that mitigates this problem. It facilitates obtaining data with a spatial sampling density, which is rarely possible with standard instrumentation on land, and it only requires moderate logistical effort. A unique field study on a shallow volcanic lake demonstrated that this method is feasible with only a minor loss of accuracy when compared to anchored and land soundings. We found that the noise sources arising from the moving instrument and the boat engine can be neglected. The field survey was performed on the Lagoa das Furnas (São Miguel, Azores Islands, Portugal), which is located within an active volcanic area and is characterized by fumarolic fields and degassing. Thus, the associated hydrothermal system is expected to extend below the lake. However, the character, geometry, and extent of this system are unknown because of the lack of boreholes and geophysical studies. In total, 600 soundings, combining towed profiles with anchored and land-based soundings, were acquired with an aim of imaging the hydrothermal system beneath the lake down to 200 m. The results from all three types of measurements compare well and thus led to consistent 1D inversion models. The inversion results delineate a highly conductive, smectite-rich cap layer dipping below the lake away from the main fumarole zone. Near this zone, the extent of the conductor agrees well with an area of intense dispersed degassing, which appears to be controlled by at least two electrically distinctive fault zones in which the conductor is found at greater depths.