An understanding of the interactions between biological, chemical and physical dynamics is especially important for the adequate conservation of the Underwater Cultural Heritage. However, while physical and chemical processes are relatively well-investigated, the biological communities associated with these habitats are poorly studied. We compared the sessile community developed on panels of different materials placed on two historical shipwrecks, the Fougueux and the Bucentaure, from the Battle of Trafalgar (October 1805). Six materials used at the construction of vessels at the 18th and 19th centuries were selected: copper, brass, cast iron, carbon steel, pine and oak. The sessile community developed on the panels was studied two and 15 months after their immersion at the water to determine the effects of materials and environmental conditions (sediments, waves, hydrodynamic conditions, temperature and salinity) on ecological succession and the possible implications at the conservation of historical shipwrecks. On the Fougueux, the environmental conditions more strongly influenced the biological succession than the material type, with pioneer colonisers dominating the communities in both sampling periods. On the Bucentaure, exposed to more stable environmental conditions, the sessile community showed differences between sampling periods and among materials at the end of the experiment. Under these more stable environmental conditions, the material type showed a higher influence on the sessile community. Species that produce calcareous concretions developed on metallic panels, but were absent on wood panels, where the shipworm Teredo navalis was more abundant. The relationship between environmental conditions, sessile organisms and material type can influence the conservation status of the archaeological sites.