The Mediterranean Sea is a large marine ecosystem with high heterogeneity in both environmental and ecological characteristics. It presents clear gradients from north to south and west to east. It is also an important area in terms of biodiversity and conservation of vulnerable species, and it suffers from several cumulative human impacts, such as fishing and climate change. Previous studies have characterized spatial and temporal patterns of species distributions and biodiversity indicators. However, a comprehensive analysis combining a wide representation of biodiversity indicators is still missing. In this study, we examined spatial and temporal changes of marine communities along a latitudinal gradient over the continental shelf ecosystems (25–500 m depth) of the Western Mediterranean Sea, from the Gulf of Lion in the north to the Gibraltar Strait in the south. We used information from the MEDITS trawl scientific surveys from 1994 to 2018, and we calculated relevant indicators to investigate spatial and temporal patterns in the region. We selected several indicators measuring alpha (species richness, Shannon diversity index and Pielou evenness index) and beta (decomposing both turnover and nestedness) diversity, as well as previously studied indicators identified to be sensitive to fishing and climate change impacts (biomass-based and trophic-level based metrics). We assessed differences in these indicators for the surveyed community as a whole and for fish, crustaceans and cephalopods, separately, over five regions. Our results show clear latitudinal gradients in some indicators: we observe a reversed pattern between richness (decreasing from south to north) and biomass trends (increasing from south to north) for the demersal community. We also found a generalized increase in β-diversity in most regions with time, and a decline in the trophic level of the surveyed community. In addition, we identify a remarkable increase in several indicators when only considering the cephalopods group, and a general low environmental status for the North Catalan Sea. We discuss our results considering the differences between regions and taxa related to the fishing activity and environmental dynamics that can act at different scales. This in-depth analysis illustrates how to use a selection of indicators that combine the capacity to detect ecological changes from regional to sub-regional scales.