Hydrothermal alteration processes involve mineralogical, chemical, and textural changes as a result of hot aqueous fluid-rock interaction under evolving boundary conditions. These changes affect the physico-chemical properties of the rocks, enabling high-resolution geophysical prospecting to be an important tool in the detection of seafloor hydrothermal alteration. Here we present the results of recent geophysical investigations of the Marsili and Palinuro volcanic complexes, southern Tyrrhenian Sea, during the 2010 TIR10 and 2011 MAVA2011 cruises by the R/V Urania. The new dataset includes a dense grid of multibeam bathymetry; seafloor reflectivity, magnetic and gravity lines; and high-resolution single (CHIRP) and multichannel seismic profiles. The surveys were focused on areas known to host intense hydrothermal alteration in order to provide a more detailed description of the Marsili and Palinuro hydrothermal systems. Ground-truthing was based on earlier discoveries of hydrothermal vents and their associated deposits, and on direct observations made by ROV dives. High-resolution morpho-bathymetry, sonar reflectivity, rock magnetization, and density distribution together enabled us to assess the extent of seafloor hydrothermal alteration and its relationship to local volcanic and tectonic structures. Hydrothermal alteration associated with the Marsili seamount is largely distributed along primary volcano-tectonic structures at the ridge crest. By contrast, at Palinuro hydrothermal alteration is mostly associated with secondary volcanic structures such as collapsed calderas and volcanism reactivation along ring faults. In particular, evidence for intense hydrothermal activity occurs at Palinuro where volcanotectonic features interact with regional tectonic structures.