Breakwaters are man-made constructions utilised for preventing coastal erosion primarily from wave action. At the same time defence structures, modifying currents and circulation, can affect water quality and benthic assemblages. Assessing and minimizing the impact of these structures is a priority in human-modified coastal ecosystems, such as the central northern Adriatic where breakwaters extend for hundreds of km. We investigated the effects of breakwater relocation on benthic features and meiofaunal diversity. To do this we conducted a before-after comparison (2011-2017) the relocation, which occurred in 2015. The analysis was conducted comparing a sheltered site, characterized by the presence of seagrass meadows and a wave-exposed site. Sediment features and meiofaunal variables were altered by the relocation, especially in the areas colonised by seagrass meadows. Results presented here pointed out an enrichment in organic matter, the loss of two sensitive taxa (Cumacea and Ostracoda) and a shift in the assemblage structure with the increase of the relevance of Copepoda and Polychaeta. These results indicate that the careful management of breakwater is crucial for planning adequate conservation practises and protecting seagrass habitats and their biodiversity.