Data and codes for: Macrophytes and Environmental Drivers in Transitional Waters: A 13-Year Assessment Integrating MaQI and Multivariate Analyses

Transitional water bodies are highly dynamic ecosystems where macrophyte communities integrate environmental variability over space and time. This study assessed macrophyte assemblages, ecological status (MaQI), and physical and chemical conditions across eleven Mediterranean transitional water bodies over a 13-year monitoring period (Apulian region, Southern Italy). Macrophyte diversity showed marked spatial heterogeneity, ranging from species-rich, marine-influenced basins to shallow, nutrient-enriched systems dominated by opportunistic taxa. Multivariate analyses (PCA and CCA) identified salinity, depth, temperature, and nutrient conditions as major drivers of macrophyte distribution, although ecological status exhibited only weak alignment with these gradients. Temporal trajectories of MaQI revealed overall stability at the regional scale but pronounced basin-specific variability, with persistent high status in Porto Cesareo and recent declines in Lesina (LE01). These findings highlight the strong environmental differentiation among basins and emphasise the value of integrating macrophyte-based indices with multivariate ecological analyses to improve ecological assessment and support adaptive management of transitional ecosystems.