The Ligurian Sea is a deep basin in the northernmost sector of the western Mediterranean which shows peculiar hydrodynamic and meteo-oceanographic features. The coasts of the Ligurian Sea are among the most urbanised and industrialised along the Italian coastline: the main causes of disturbance being littoral urban development and harbour activities, the building of littoral rail- and highways, and the presence of several polluted discharges. This review, by evaluating the huge scientific output published in the last three decades, describes and discusses the most important geological, hydrological and biological characteristics of the Ligurian Sea. We show that this regional sea has largely been investigated in terms of its geological and structural evolution, as well as in terms of the sedimentation dynamics of the littoral and deep bottoms, with particular attention to the sedimentation balance of the beaches and their erosive processes. We report that the prevalent hydrodynamic and meteo-oceanographic conditions favour a continuous exchange of coastal water masses, and that the seasonal and interannual dynamics of water masses can effects the local climate, with direct and indirect consequences on fish and benthic communities documented in the last decade. We stress that although recent studies offer good knowledge of the distribution of coastal benthic communities, only scant information is available for the whole continental shelf, the submarine canyons and the rocky bathyal bottoms. Our meta-analysis reveals that significant fishing activities are monitored, but also that certain sectors of the biological resource are suffering, and suggests the set up of appropriate management measures. The Ligurian Sea hosts a number of Marine Protected Areas (MPAs) of high relevance, while the institution of the Whale Sanctuary completes the protection policy of the Regione Liguria. Our meta-analysis points out the need for long-term studies, based primarily on the analysis of those areas of the Ligurian Sea that have been little investigated to date. Finally, only properly addressed studies, using experimental approaches and along appropriate spatial and temporal scales, might allow us to understand the functioning of the Ligurian marine ecosystems, evaluate their health conditions and the dynamics of the main variables that affect the distribution of the single species (including species of high economic value) and benthic communities.