In this work, we integrate five case studies harboring vulnerable deep-sea benthic habitats in different geological settings from mid latitude NE Atlantic Ocean (24–42° N). Data and images of specific deep-sea habitats were acquired with Remoted Operated Vehicle (ROV) sensors (temperature, salinity, potential density, O2, CO2, and CH4). Besides documenting some key vulnerable deep-sea habitats, this study shows that the distribution of some deep-sea coral aggregations (including scleractinians, gorgonians, and antipatharians), deep-sea sponge aggregations and other deep-sea habitats are influenced by water masses’ properties. Our data support that the distribution of scleractinian reefs and aggregations of other deep-sea corals, from subtropical to north Atlantic could be dependent of the latitudinal extents of the Antarctic Intermediate Waters (AAIW) and the Mediterranean Outflow Waters (MOW). Otherwise, the distribution of some vulnerable deep-sea habitats is influenced, at the local scale, by active hydrocarbon seeps (Gulf of Cádiz) and hydrothermal vents (El Hierro, Canary Island). The co-occurrence of deep-sea corals and chemosynthesis-based communities has been identified in methane seeps of the Gulf of Cádiz. Extensive beds of living deep-sea mussels (Bathymodiolus mauritanicus) and other chemosymbiotic bivalves occur closely to deep-sea coral aggregations (e.g., gorgonians, black corals) that colonize methane-derived authigenic carbonates.