Submarine hydrothermal activity is responsible for heat and chemical exchanges through the seafloor. Shallow-water hydrothermal systems (SWHS), while identified around the globe, are often studied in a way that is less comprehensive than their deep-ocean counterparts (e.g., along ridges), where systematic optical and acoustic mapping is more prevalent and coupled to in situ observations and sampling. Using aerial drones, an AUV, and temperature measurements at 10–40 cm subseafloor, we investigated in 2019 one of the most extensive SWHS known to date, in Paleochori and nearby Spathi and Agia Kyriaki Bays (south of Milos, Greece). Hydrothermal venting, found from the shore to water depths of almost 500 m, shows emissions of gases and high-temperature fluids, often associated with bacterial mats and/or hydrothermal mineral precipitates. This study provides extensive drone mapping coupled with local AUV surveys for seafloor characterization and ground-truthing from the shore to ~20 m water depth. Seafloor photomosaics also provide a detailed context to samples, measurements and observations carried in situ. We interpret the photomosaics to define distinct seafloor types, linked to this hydrothermal activity. White hydrothermal patches (WHPs) often show a clear polygonal organization, together with outflow areas that are both more dispersed and distributed. Polygonal patterns likely result from fluid convection in a sandy porous medium heated from below. These WHPs display elevated subseafloor temperatures, typically >50°C, with maximum values of ~75°C. Photomosaics also display textures of biological origin, including seagrass and bioturbation patterns. Widespread bioturbation by burrowing shrimps is often associated with WHPs, bounding them, but also occurs on sandy seafloor away from hydrothermal patterns. Subseafloor temperatures at these bioturbated areas are of ~30–40°C, and are thus transitional between hot WHPs and sedimented seafloor unaffected by hydrothermal activity (~24°C). In addition to linking subseafloor temperature data and interpreted seafloor photomosaics, our results provide a comprehensive general overview of this SWHS, of the organization of its hydrothermal outflow through the seafloor, and of the underlying subseafloor fluid circulation. This paper also gives the first perspectives on the heat fluxes of the system, and constitutes a background for other studies on the nature and distribution of microbial communities, controlled by this hydrothermal activity.