The Eiffel Tower hydrothermal edifice is a large structure of ~450 m² located at a depth of 1700 m in the South-East of the Lucky Strike hydrothermal vent field. Since the deployment of the EMSO-Azores observatory in 2010, the edifice has been repeatedly surveyed with the remotely operated vehicle Victor6000 for inter-annual monitoring. Video transects were collected with a forward-looking camera in 2015, 2018 and 2020. Video sequences were used to build 3D models of the edifice using structure-from-motion techniques. Surface of substrata, vent megafaunal assemblages, microbial mat and the position of hydrothermal vent outflows and topographic changes were digitised over the 3D models for each side of the edifice. These variables were used to investigate scales of ecological dynamics over space and time. Hereby, we provide the dataset as well as a method to extract and visualise data in open-source software (R).