The occurrence of hydrothermal vent ecosystems at Secca delle Fumose, Pozzuoli Bay (Gulf of Naples), represented an opportunity to study the benthic assemblages under the thermal stress of hydrothermal emissions in a very shallow environment (9–14 m water depth). In autumn 2016, the macrobenthic community was sampled by scuba divers at four sites located in the Baia Underwater Archeological Park. Two sites were characterized by vent emissions (one with white bacterial mat scattered on the bottom and one with a yellow substrate around a geyser opening) and two at about 100 m away, used as control. Sediment and interstitial water environmental variables were measured to determine their influence on the structure of macrobenthic assemblages. A total of 1,954 macrofaunal individuals was found, characterized by great differences in abundance and species richness among sites. This pattern was correlated to the dominance of a particular set of variables that drastically change in a very small spatial scale, from one site to another. The control sites, characterized by the highest percentage of gravel in the sediments (19.67 ± 2.6%) and normal level of major ions such as Ca2+, K+, and Mg2+ in the interstitial waters, showed the highest values of sinecological indices. The “white” hydrothermal site exhibited the lowest species richness, abundance and species diversity, influenced by low pH values (∼7.6), high temperatures (∼37.53°C) and by the highest total organic carbon content (TOC 34.78%) in the sediment. The “yellow” hydrothermal site, with sediment TOC equal to 30.03% and interstitial sulfide ions measuring 130.58 ppm, showed higher values of sinecological indices than those recorded at the “white” site. Therefore, taxonomic analysis revealed a high turnover between control and vents sites. This highlights the preference for hydrothermal vents by a few resistant species, such as the gastropod Tritia cuvierii and the polychaete Capitella capitata, confirming the role of the latter species as opportunistic in extreme environments like Secca delle Fumose.