A harmonized individual-level phytoplankton trait dataset from Mediterranean and Black Sea transitional waters.

Background: Transitional waters are dynamic coastal ecosystems located at the interface between freshwater and marine environments. They are characterized by pronounced environmental variability resulting from the interaction between geomorphology, freshwater inputs, tidal exchanges, climatic variability, and human activities. These factors generate high habitat heterogeneity and complex ecological dynamics.Phytoplankton communities inhabiting transitional waters are particularly sensitive to both natural gradients and anthropogenic pressures, often exhibiting marked spatial and seasonal patterns in species composition, abundance and functional structure. In response to fluctuating environmental conditions, phytoplankton taxa display a wide range of morphometric and functional adaptations, making trait-based approaches especially suitable for investigating community organization and ecosystem functioning in these ecosystems.Although a large amount of phytoplankton trait data is available, its use could be enhanced through improved data harmonization and interoperability. The availability of FAIR (Findable, Accessible, Interoperable and Reusable) phytoplankton trait data from transitional waters, coupled with associated environmental information, is therefore essential to support comparative analyses and to improve our understanding of trait-environment relationships in these vulnerable ecosystems. New information: In this study, we present two complementary and FAIR datasets derived from coordinated monitoring activities conducted in transitional water ecosystems across the Mediterranean and Black Sea regions. The phytoplankton dataset comprises individual-level morpho-functional trait measurements collected at 14 sites, including 104,687 records from 242 taxa belonging to 10 phyla. Recorded traits include cell size, shape, density, biovolume and estimated carbon content and biomass values, enabling analyses at multiple levels of biological organization, from individuals to functional guilds and whole communities. The abiotic dataset includes in situ measurements of key physicochemical variables describing water quality conditions, such as salinity, conductivity, temperature, pH, dissolved oxygen, oxygen saturation and total dissolved solids. Nutrient concentrations are also provided, including nitrite (NO₂), nitrate (NO₃), ammonium (NH₄), dissolved inorganic nitrogen, phosphate (PO₄) and silicate (SiO₂). In addition, the dataset also includes information, when available, on the main physiographic and hydrological characteristics of the studied transitional waters, including water depth, tidal range, inlet morphology (outlet length and width), sinuosity index, surface area and hydrological connectivity. Qualitative descriptors of anthropogenic pressure and protection status are also included, such as the presence of Ramsar designation, Natura 2000 sites, local protection plans and indicators of human disturbance. Together, these variables characterize microtidal, nutrient-rich lagoon ecosystems that differ in their environmental conditions and degrees of anthropogenic impact, providing a comprehensive environmental context for trait-based analyses of phytoplankton communities.Both datasets have been harmonized to ensure semantic consistency, interoperability and reusability. They are accompanied by comprehensive metadata and are openly accessible through the LifeWatch Italy Data Portal and Metadata Catalogue (doi: https://doi.org/10.48372/x9qx-4t72). Data quality and usability have been validated through their application in previously published studies focusing on morpho-functional analyses, phytoplankton guild classification and hypothesis testing across different levels of data aggregation. Together, these FAIR-compliant datasets represent a robust and reusable resource for advancing trait-based research and functional ecology in dynamic transitional water ecosystems.