This work presents refined, updated subregional and regional non-indigenous species (NIS) inventories for the Mediterranean Sea, validated by national and taxonomic experts, with species records observed until December 2020. These datasets will be used as the baselines for the implementation of the Integrated Monitoring and Assessment Programme for the Mediterranean (IMAP) and the Mediterranean Quality Status Report 2023. In total, 1006 non-indigenous species have been found in Mediterranean marine and brackish waters. The highest numbers of NIS were observed in Israel, Türkiye, Lebanon and Italy. Approximately 45 species were categorized as data deficient, either due to lack of consensus on their alien status or the validity of their identification. Polychaeta, Foraminifera and macroalgae were the groups with the highest numbers of controversial species. There was a general increase in the yearly rate of new NIS introductions after the late 1990s, which appears to be slowing down in the last decade, but this may be confounded by reporting lags and differential research efforts. Between 1970 and 2020 there has been a steep increase in the proportion of shared species present throughout all four Mediterranean subregions, which are predominantly transported via shipping and recreational boating. While Lessepsian species are gradually spreading westwards and northwards, there is still a considerable invasion debt accumulating in the eastern and central Mediterranean.

Invasive alien species are a major worldwide driver of biodiversity change. The current study lists verified records of non-indigenous species (NIS) in European marine waters until 2020, with the purpose of establishing a baseline, assessing trends, and discussing appropriate threshold values for good environmental status (GES) according to the relevant European legislation. All NIS records were verified by national experts and trends are presented in six-year assessment periods from 1970 to 2020 according to the European Union Marine Strategy Framework Directive. Altogether, 874 NIS have been introduced to European marine waters until 2020 with the Mediterranean Sea and North-East Atlantic Ocean hosting most of the introductions. Overall, the number of new introductions has steadily increased since 2000. The annual rate of new introductions reached 21 new NIS in European seas within the last six-year assessment period (2012–2017). This increase is likely due to increased human activities and research efforts that have intensified during the early 21st century within European Seas. As Europe seas are not environmentally, nor geographically homogenous, the setting of threshold values for assessing GES requires regional expertise. Further, once management measures are operational, pathway-specific threshold values would enable assessing the effectiveness of such measures.

Globally, marine bioinvasions threaten marine ecosystem structure and function, with the Mediterranean Sea being one of the most affected regions. Such invasions are expected to increase due to climate change. We conducted a risk screening of marine organisms (37 fishes, 38 invertebrates, and 9 plants), both extant and ‘horizon’ (i.e., not present in the area but likely to enter it). Based on expert knowledge for the Eastern Adriatic Sea coasts of Slovenia, Croatia, and Montenegro, screenings were conducted under both current and predicted climate conditions indicating with an increase in sea surface temperature and salinity of the Adriatic Sea together with changes in precipitation regime. Our aims were to: (1) identify non-native extant and horizon marine species that may pose threats to native biodiversity and (2) evaluate the risk of invasiveness of the selected species under current and predicted climate conditions. Of the 84 species screened, there was an increase in those ranked as ‘high risk’ from 33 (39.3%) under current climate conditions and to 47 (56.0%) under global warming scenarios. For those ranked as ‘very high’ risk, the increase was from 6 (7.1%) to 21 (25.0%). Amongst the screened species, the already established high-risk species Pacific oyster Magallana gigas and Atlantic blue crab Callinectes sapidus represent a threat to ecosystem services. Given the under-representation of marine species in the current European Union List, the species we have ranked as high to very high risk should be included.

Marine phanerogams are considered biological sentinels or indicators since any modification in seagrass meadow distribution and coverage signals negative changes in the marine environment. In recent decades, seagrass meadows have undergone global losses at accelerating rates, and almost one-third of their coverage has disappeared globally. This study focused on the dynamics of seagrass meadows in the northern Adriatic Sea, which is one of the most anthropogenically affected areas in the Mediterranean Sea. Seagrass distribution data and remote sensing products were utilized to identify the stable and dynamic parts of the seagrass ecosystem. Different seagrass species could not be distinguished with the Sentinel-2 (BOA) satellite image. However, results revealed a generally stable seagrass meadow (283.5 Ha) but, on the other hand, a stochastic behavior in seagrass meadow retraction (90.8 Ha) linked to local environmental processes associated with anthropogenic activities or climate change. If systemized, this proposed approach to monitoring seagrass meadow dynamics could be developed as a spatial decision support system for the entire Mediterranean basin. Such a tool could serve as a key element for decision makers in marine protected areas and would potentially support more effective conservation and management actions in these highly productive and important environments.

Molecular methods such as DNA/eDNA metabarcoding have emerged as useful tools to document the biodiversity of complex communities over large spatio‐temporal scales. We established an international Marine Biodiversity Observation Network (ARMS‐MBON) combining standardised sampling using autonomous reef monitoring structures (ARMS) with metabarcoding for genetic monitoring of marine hard‐bottom benthic communities. Here, we present the data of our first sampling campaign comprising 56 ARMS units deployed in 2018–2019 and retrieved in 2018–2020 across 15 observatories along the coasts of Europe and adjacent regions. We describe the open‐access data set (image, genetic and metadata) and explore the genetic data to show its potential for marine biodiversity monitoring and ecological research. Our analysis shows that ARMS recovered more than 60 eukaryotic phyla capturing diversity of up to ~5500 amplicon sequence variants and ~1800 operational taxonomic units, and up to ~250 and ~50 species per observatory using the cytochrome c oxidase subunit I (COI) and 18S rRNA marker genes, respectively. Further, ARMS detected threatened, vulnerable and non‐indigenous species often targeted in biological monitoring. We show that while deployment duration does not drive diversity estimates, sampling effort and sequencing depth across observatories do. We recommend that ARMS should be deployed for at least 3–6 months during the main growth season to use resources as efficiently as possible and that post‐sequencing curation is applied to enable statistical comparison of spatio‐temporal entities. We suggest that ARMS should be used in biological monitoring programs and long‐term ecological research and encourage the adoption of our ARMS‐MBON protocols.